A día de hoy, la relación causal entre la dieta y las complicaciones hepáticas continúa siendo una incógnita. En este estudio, se pretende investigar los efectos de 8 dietas sobre la expresión de genes relacionados con las vías metabólicas intermedias del hígado. Para ello, se han utilizado ejemplares masculinos adultos de ratón que han sido alimentados durante 3 semanas con la dieta correspondiente (3 por grupo) y de los cuales se han extraído muestras de tejido hepático. La expresión en estas muestras ha sido determinada mediante microarrays de un color de Affymetrix (Affymetrix Mouse 430 2.0 Gene). El procesado de los datos y la búsqueda de genes diferencialmente expresados (DEG) respecto al control se ha realizado mediante el uso del software estadístico R (versión 3.6.2) y de paquetes del proyecto BioConductor (versión 3.10). Los datos y el código relacionados con el análisis pueden ser consultados en el siguiente repositorio GitHub.
El objetivo del estudio es aportar nueva información y mejorar el conocimiento del efecto que tiene la dieta sobre la expresión, en hepatocitos, de genes relacionados con el metabolismo lipídico, la inflamación y el estrés oxidativo. En esta dirección, se pretende identificar que genes y que vías metabólicas están diferencialmente expresados en cada dieta respecto al control (AIN-93M).
Aunque existe una gran variedad de software que permite analizar datos procedentes de estudios realizados con microarrays (Mehta 2011), nosotros nos hemos decantado por la combinación de R (versión 3.6.2) y BioConductor (versión 3.10). Además, para facilitar el procesado y hacerlo más cómodo visualmente, hemos utilizado la interfaz R-Studio. En la Tabla 1 se muestra un listado con los paquetes implementados durante el análisis.
| Package | Repository | Description | Version |
|---|---|---|---|
| knitr | CRAN | Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques. | 1.28 |
| kableExtra | CRAN | Build complex HTML or ‘LaTeX’ tables using ‘kable()’ from ‘knitr’ and the piping syntax from ‘magrittr’. | 1.1.0 |
| citr | CRAN | Functions and an ‘RStudio’ add-in that search ‘Bib(La)TeX’-files or ‘Zotero’ libraries to insert formatted Markdown citations into the current document. | 0.3.2 |
| ggplot2 | CRAN | A system for ‘declaratively’ creating graphics, based on “The Grammar of Graphics”. | 3.3.0 |
| ggrepel | CRAN | Provides text and label geoms for ‘ggplot2’ that help to avoid overlapping text labels. Labels repel away from each other and away from the data points. | 0.8.2 |
| gplots | CRAN | Various R programming tools for plotting data. | 3.0.3 |
| readxl | CRAN | Import excel files into R. Supports ‘.xls’ via the embedded ‘libxls’ C library and ‘.xlsx’ via the embedded ‘RapidXML’ C++ library . | 1.3.1 |
| viridis | CRAN | Implementation of the ‘viridis’ - the default -, ‘magma’, ‘plasma’, ‘inferno’, and ‘cividis’ color maps for ‘R’. | 0.5.1 |
| cowplot | CRAN | Provides various features that help with creating publication-quality figures with ‘ggplot2’. | 1.0.0 |
| RColorBrewer | CRAN | Creates nice looking color palettes especially for thematic maps. | 1.1-2 |
| magritrr | CRAN | The magrittr is a package with two aims: to decrease development time and to improve readability and maintainability of code. | 1.5 |
| Biobase | BioConductor | Functions that are needed by many other packages or which replace R functions. | 2.46.0 |
| oligo | BioConductor | A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. | 1.50.0 |
| arrayQualityMetrics | BioConductor | This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). | 3.42.0 |
| genefilter | BioConductor | Some basic functions for filtering genes. | 1.68.0 |
| mouse4302.db | BioConductor | A package containing an environment representing the Mouse430_2.cdf file. | 3.2.3 |
| limma | BioConductor | Data analysis, linear models and differential expression for microarray data. | 3.42.2 |
| annaffy | BioConductor | Functions for handling data from Bioconductor Affymetrix annotation data packages. | 1.58.0 |
| EnhancedVolcano | BioConductor | Here, we present a highly-configurable function that produces publication-ready volcano plots. | 1.4.0 |
| ReactomePA | BioConductor | This package provides functions for pathway analysis based on REACTOME pathway database. | 1.30.0 |
| enrichplot | BioConductor | The ‘enrichplot’ package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. | 1.6.1 |
| DOSE | BioConductor | This package implements five methods for measuring semantic similarities among DO terms and gene products. | 3.12.0 |
Tabla 1: lista de paquetes utilizados durante el análisis.
Los datos utilizados para el análisis provienen de un estudio publicado por Renaud (2014). Estos, se encuentran disponibles en la base de datos GEO (Gene Expression Omnibus), un servidor web que subministra, entre otros, datos relacionados con experimentos realizados con microarrays. Desde GEO, podemos acceder a nuestros datos mediante el código alfanumérico siguiente: GSE51885. Además, una vez abierta la página principal del estudio, podemos descargar los archivos .CEL correspondientes a cada uno de los arrays (GSE51885_RAW.tar).
El estudio que generó estos datos investigaba el efecto, respecto al control, de 8 dietas (Tabla 2) en la expresión de genes de las vías metabólicas intermedias del hígado. Para ello, ejemplares de ratones macho adultos (3 réplicas) fueron alimentados durante 3 semanas con una de las dietas siguientes:
TD.94048 (CT): AIN-93M purified diet (control diet)
TD.8604 (LAR): Natural ingredient diet (used in our animal facility) (Lab chow)
TD.89247 (FR): 60% fructose diet
TD.97070 (HF): High-fat diet
TD.88137 (AC): High-saturated fat and sucrose diet (Western diet)
TD.02028 (AR): High-fat, sucrose, cholesterol, and cholic acid (CA) diet (atherogenic diet)
TD.8422 (EFA): Essential fatty acid (EFA) deficient diet
TD.00235 + 7% sunflower oil (DHA): low n-3 diet (Levant 2006)
Diet restriction (DR): 75% of the diet TD.8604 consumed by ad lib feeding (Varady 2007)
| Composition | AIN.93Purified | LabChow | HighFructose | HighFat | Western | Atherogenic | EFA.Deficient | Low.n.3 |
|---|---|---|---|---|---|---|---|---|
| Fat (g/kg) | 39.4 | 41 | 50 | 329.0 | 209 | 209 | 50 | 67.20 |
| Saturated | 6.0 | 9 | 19 | 151.0 | 136 | 136 | 50 | 7.32 |
| MUFA | 9.4 | 11 | 25 | 146.0 | 66 | 66 | 0 | 12.84 |
| PUFA | 24.0 | 21 | 6 | 32.0 | 7 | 7 | 0 | 43.34 |
| n-6:n-3 PUFA | 6.7 | 12 | 10.4 | 20.9 | 6 | 6 | No n-3 or n-6 | 134.40 |
| Carbohydrates (g/kg) | 684.0 | 402 | 6–4 | 271.0 | 485 | 469 | 665 | 646.00 |
| Sucrose (g/kg) | 107.0 | Very little | 0 | 175.0 | 345.6 | 329.6 | 660.3 | 117.10 |
| Fructose (g/kg) | 0.0 | Very little | 600 | 0.0 | 0 | 0 | 0 | 0.00 |
| Polysaccharide (g/kg) | 577.0 | majority | 4 | 96.0 | 139.4 | 139.4 | 4.7 | 528.90 |
| Cholesterol (mg/kg) | 28.0 | 50 | 89 | 54.0 | 2,077 | 13,077 | 8 | 40.00 |
| Protein (g/kg) | 124.0 | 243 | 183 | 239.0 | 173 | 173 | 176 | 190.00 |
| Cholic acid (g/kg) | 0.0 | 0 | 0 | 0.0 | 0 | 5 | 0 | 0.00 |
| Kcal/g | 3.6 | 3 | 3.6 | 5.1 | 4.5 | 4.5 | 3.8 | 3.80 |
Tabla 2: composición de 8 de las dietas (incluyendo el control) utilizadas en el estudio. La novena dieta (DR), contiene la misma composición que la dieta LAR.
A continuación, los ratones fueron eutanizados (8:00-10:00 A.M), obteniéndose muestras de sangre y de tejido hepático. De las muestras de tejido hepático se extrajo y se purificó el ARN total mediante en el uso de los reactivos RNAzol B y RNA Bee respecitvamente (Tel-Test Inc., Friendswood, TX). Seguidamente, se cuantificó la concentración de ARN (\(\lambda\) = 260 nm) utilizando un espectrofotómetro NanoDrop1000 (NanoDrop Technologies, Wilmington, DE) y se evaluó la integridad de las muestras mediante electroforesis. La expresión génica de cada muestra fue determinada mediante el uso de microarrays de un color del tipo Affymetrix Mouse 430 2.0 Gene. Todos los protocolos utilizados fueron aprovados por el IACUC (Institutional Animal Care and Use Committee).
En síntesis, nos encontramos frente a un diseño factorial con un factor (Dieta) de 9 niveles. Cada nivel conforma una única unidad experimental compuesta de tres réplicas biológicas (3 ratones) y, por lo tanto, el tamaño muestral del experimento es de 27 muestras.
El análisis de datos de microarrays se puede realizar siguiendo protocolos muy variables (Klaus 2018; Depiereux 2015; Gan 2014). En esta sección del informe se intenta resumir el workflow estándar de uno de estos análisis proponiendo métodos específicos para cada uno de los pasos.
Para facilitar el análisis, intentaremos almacenar todos los datos de origen y los resultados generados siguiendo un criterio lógico de ordenación. En esta dirección, crearemos un pequeño subconjunto de directorios dentro de nuestro directorio de trabajo (C:/Users/USER/Documents/Màster Bioestadística i Bioinfo/Análisis de datos Ómicos/PECS/ADO_PEC1_Marc_Garcia). Básicamente este subconjunto estará formado por los cuatro directorios siguientes:
.CEL y el archivo targets.La preparación de los datos para su análisis implica, normalmente, un primer paso que consiste en la construcción de un objeto de tipo ExpressionSet a partir de los ficheros .CEL y el archivo targets.csv. Los primeros contienen los valores de fluorescencia de cada array (raw data) mientras que el segundo (Tabla 3) relaciona cada array con la muestra y el grupo al que pertenece y las covariables que lo definen. Nosotros, para generar este objeto, nos ayudaremos de función read.celfiles() del paquete oligo (Carvalho 2010).
| FileName | Title | Group | ShortName |
|---|---|---|---|
| GSM1254691.CEL | 60% Fructose 1 | FR | FR.1 |
| GSM1254692.CEL | 60% Fructose 2 | FR | FR.2 |
| GSM1254693.CEL | 60% Fructose 3 | FR | FR.3 |
| GSM1254694.CEL | Adjusted Calories 1 | AC | AC.1 |
| GSM1254695.CEL | Adjusted Calories 2 | AC | AC.2 |
| GSM1254696.CEL | Adjusted Calories 3 | AC | AC.3 |
| GSM1254697.CEL | AIN-93M Purified (Control) 1 | CT | CT.1 |
| GSM1254698.CEL | AIN-93M Purified (Control) 2 | CT | CT.2 |
| GSM1254699.CEL | AIN-93M Purified (Control) 3 | CT | CT.3 |
| GSM1254700.CEL | Atherogenic Rodent 1 | AR | AR.1 |
| GSM1254701.CEL | Atherogenic Rodent 2 | AR | AR.2 |
| GSM1254702.CEL | Atherogenic Rodent 3 | AR | AR.3 |
| GSM1254703.CEL | Current LAR Diet 1 | LAR | LAR.1 |
| GSM1254704.CEL | Current LAR Diet 2 | LAR | LAR.2 |
| GSM1254705.CEL | Current LAR Diet 3 | LAR | LAR.3 |
| GSM1254706.CEL | DHA-supplemented 1 | DHA | DHA.1 |
| GSM1254707.CEL | DHA-supplemented 2 | DHA | DHA.2 |
| GSM1254708.CEL | DHA-supplemented 3 | DHA | DHA.3 |
| GSM1254709.CEL | Diet-restriction 1 | DR | DR.1 |
| GSM1254710.CEL | Diet-restriction 2 | DR | DR.2 |
| GSM1254711.CEL | Diet-restriction 3 | DR | DR.3 |
| GSM1254712.CEL | EFA Deficient 1 | EFA | EFA.1 |
| GSM1254713.CEL | EFA Deficient 2 | EFA | EFA.2 |
| GSM1254714.CEL | EFA Deficient 3 | EFA | EFA.3 |
| GSM1254715.CEL | High Fat 1 | HF | HF.1 |
| GSM1254716.CEL | High Fat 2 | HF | HF.2 |
| GSM1254717.CEL | High Fat 3 | HF | HF.3 |
Tabla 3: contenido del fichero targets.csv.
Una vez creado el ExpressionSet con los “datos crudos”, es necesario realizar un primer control para determinar si nuestros datos tienen la calidad suficiente para ser normalizados y posteriormente analizados. Aunque existen gran cantidad de métodos alternativos, una opción muy interesante consiste en utilizar la función arrayQualityMetrics() del paquete con el mismo nombre (Kauffmann 2009). Básicamente, esta función realiza el control de calidad automáticamente y crea un nuevo directorio con los resultados. Este directorio incluye, además de las figuras correspondientes a cada una de las pruebas, un informe dinámico en formato html (index.html). Para complementar el output de arrayQualityMetrics(), generaremos un boxplot y un PCA plot. Mientras que para el boxplot utilizaremos la función boxplot() del paquete stats (RCoreTeam 2019), para el PCA plot crearemos nuestra propia función (Figura S1).
Una vez eliminados los arrays defectuosos se deben normalizar los datos. De este modo, minimizaremos la variabilidad de las muestras debida a razones no biológicas y permitiremos la comparación entre chips. Nosotros hemos aplicado el método RMA (Robust Multichip Average), uno de los más extendidos y utilizados entre la comunidad científica (Irizarry 2003). Para implementarlo hemos hecho uso de la función rma() del paquete oligo (Carvalho 2010).
Aunque no es imprescindible, después de la normalización de los datos, podemos realizar un segundo control de calidad que determine si la normalización ha funcionado. De nuevo, utilizaremos la función arrayQualityMetrics() y combinaremos su output con un PCA plot y un boxplot que elaboraremos nosotros manualmente.
Previamente a la selección de genes diferencialmente expresados, con el objetivo de minimizar el problema de la multiplicidad de tests, es común eliminar aquellos probesets/tránscritos de los cuales no se espera que presenten diferencias entre grupos. Normalmente, el modus operandi consiste en construir un primer gráfico (SD plot) de la desviación estándar total de cada probeset/tránscrito contra su posición en el ranking de variabilibad (de menos a más variable). De este modo, podemos establecer un punto de corte que determinará la proporción que nos quedaremos y la proporción que eliminaremos. Una vez establecido este threshold, nosotros utilizaremos la función nsFilter() del paquete genefilter (Gentleman 2019) para hacer el filtrado. Adicionalmente, si así lo deseamos, podemos eliminar también mediante esta función los probesets duplicados o aquellos para los cuales no se dispone de anotación.
Con la intención de identificar que genes estan diferencialmente expresados entre cada una de las dietas y el control, podemos utilizar diferentes enfoques (Chrominski 2015). Para comparaciones entre dos condiciones o grupos se han utilizado clásicamente pruebas t o variantes de ellas (Tsai 2003; Draghici 2001). Sin embargo, los modelos lineales basados en el análisis de la varianza funcionan cuando establecemos una comparación entre más de dos grupos y además han demostrado ser significativamente más robustos que las pruebas t (Smyth 2004). Nosotros, para este análisis utilitzaremos el paquete de Bioconductor limma (Smyth 2015). A continuación se describen brevemente todos los pasos necesarios para generar el modelo lineal e identificar y visualizar aquellos genes que presentan una expresión diferencial entre comparaciones.
El primer paso es la construcción de la matriz de diseño, una tabla que muestra la localización de cada una de las muestras respecto a los grupos o unidades experimentales (Tabla 4). Para construirla utilizaremos la función model.matrix() del paquete stats (RCoreTeam 2019).
| X | AC | AR | CT | DHA | DR | EFA | FR | HF | LAR |
|---|---|---|---|---|---|---|---|---|---|
| FR.1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| FR.2 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| FR.3 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| AC.2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AC.3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| CT.1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| CT.2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| CT.3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| AR.1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AR.2 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AR.3 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| LAR.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| LAR.2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| LAR.3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| DHA.1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| DHA.2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| DHA.3 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| DR.1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| DR.2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| DR.3 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| EFA.1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| EFA.2 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| EFA.3 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| HF.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| HF.2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| HF.3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
Tabla 4: matriz de diseño que incluye la localización de las muestras respecto a cada grupo.
La matriz de contrastes se utiliza para describir cada uno de los contrastes que queremos realizar. Sus filas corresponden a las columnas de la matriz de diseño y sus columnas a los contrastes especificados. Los elementos involucrados en cada uno de los contrastes se marcan con 1s y -1s. Nosotros, para construir esta matriz, utilizaremos la función makeContrasts() del paquete limma (Smyth 2015). Los contrastes definidos en este estudio se muestran en la Tabla 5.
| X | CTvsFR | CTvsAC | CTvsAR | CTvsDHA | CTvsDR | CTvsEFA | CTvsHF | CTvsLAR |
|---|---|---|---|---|---|---|---|---|
| AC | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| AR | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| CT | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 |
| DHA | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| DR | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| EFA | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| FR | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| HF | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| LAR | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
Tabla 5: matriz de contrastes que incluye todos los contrastes que hemos realizado durante el análisis.
A continuación, para la construcción del modelo lineal, utilizaremos una sucesión de tres funciones del paquete limma: lmFit(), contrasts.fit() y eBayes() respectivamente (Smyth 2015). Estas tres funciones reciben como argumentos el ExpressionSet con los datos normalizados y filtrados, la matriz de diseño y la matriz de contrastes, generando un objeto de tipo MArrayLM.
El paquete limma (Smyth 2015) incluye una función muy útil que nos permite visualizar los genes diferencialmente expresados (y los que no lo están) de cada una de las comparaciones definidas por la matriz de contrastes. Nos referimos a la conocida función topTable(). Como veremos posteriormente, esta función genera tablas que contienen, para cada gen, información sobre la diferencia entre las medias grupales (logFC), la expresión media de todas las muestras (AveExpr), el valor del estadístico t (t), el p-valor (P.Value), el p-valor ajustado (adj.P.Val) y el valor del estadístico B (B). Si ordenamos los genes por p-valor o p-valor ajustado (orden ascendiente), podremos visualizar aquellos genes con una mayor evidencia de estar diferencialmente expresados.
Las tablas generadas mediante la función topTable() contienen únicamente los identificadores numéricos de los probesets/tránscritos seleccionados. Sin embargo carecen de información adicional sobre los genes a los cuales pertenecen estos identificadores. Con el objetivo de relacionar cada identificador con un gen y poblar las toptables con esta información, hemos generado la función annotatedTopTable() (Figura S2). Esta función recibe como argumentos la toptable a anotar y el paquete de anotaciones correspondiente (mouse4302.db) (Carlson 2016), añadiendo a las toptables los probeid, los símbolos de los genes, sus referencias ENTREZID y sus nombres enteros.
La visualización del contenido de las toptables se puede realizar fácilmente mediante volcano plots. Estos gráficos relacionan el cambio de expresión entre condiciones (log2 FoldChange) con la evidencia estadística (-log10(P-value)), siendo aquellos genes con valores más extremos en el eje x y con valores superiores en el eje y los que tienen una evidencia más fuerte de estar diferencialmente expresados. Una de las funciones más utilizadas para su construcción es volcanoplot() del paquete limma (Smyth 2015). Aún siendo una buena solución, nosotros hemos preferido emplear la función EnhancedVolcano() del paquete con el mismo nombre (Blighe 2019). A diferencia de volcanoplot(), EnhancedVolcano() permite dibujar el FDR y los logFC cutoffs, diferenciando las 4 categorías de genes que nos podemos encontrar mediante una paleta de colores. De este modo, es mucho más fácil identificar que genes presentan evidencia de estar diferencialmente expresados y establecer comparaciones entre los resultados de cada una de las comparaciones.
Una vez obtenida la lista de genes diferencialmente expresados al menos en una de las comparaciones, podemos utilizar técnicas de clustering para construir un heatmap que nos permita identificar que muestras o grupos presentan unos patrones de expresión más similares entre ellos. De este modo podremos definir clústers cuyo contenido podrá ser utilizado para posteriores análisis. Aunque no es la única opción, nosotros utilizaremos la fución heatmap.2() del paquete gplots (Warnes 2020). Esta función recibe como input el subset del ExpressionSet filtrado correspondiente a los genes de la lista que hemos comentado.
Ahora que ya conocemos que genes están diferencialmente expresados en almenos una de las comparaciones y, además, hemos agrupado los grupos en clústers, podemos identificar cuantos genes diferencialmente expresados respecto al control comparten los grupos de los mismos clústers. Con este objetivo, después de construir una summary table mediante la función decideTests() del paquete limma (Smyth 2015), construiremos una serie de Venn plots. Para los Venn plots utilizaremos la función vennDiagram(), también del paquete limma.
Resulta mucho más interesante y fácilmente interpretable estudiar, en vez de los genes uno por uno, que vías metabólicas están diferencialmente expresadas en cada grupo respecto al control. Para obtener esta información debemos realizar lo que se conoce como análisis de significación o análisis de pathways.
Aunque no son la única alternativa, los paquetes ReactomePA (Yu 2016) y DOSE (Yu 2015) disponen de funciones que nos permiten generar, para cada comparación, tablas que muestran las vías que presentan evidencias significativas de estar diferencialmente expresadas. Estas tablas, a las que nos vamos a referir como pathway tables contienen, para cada vía, su identificador alfa-numérico (ID), una corta descripción (Description), la proporción de genes differencialmente expresados de la comparación que están incluidos en esta vía (GeneRatio), el p-valor (pvalue), el p-valor ajustado (p.adjust) y el q-valor (qvalue). Si ordenamos las vías por p-valor o p-valor ajustado (orden ascendiente), podremos visualizar aquellas con una mayor evidencia de estar diferencialmente expresadas.
Una opción muy interesante para representar el contenido de las pathway tables consiste en construir cnetplots mediante la función cnetplot() del paquete enrichplot (Yu 2019). Estos gráficos tienen una estructura en forma de red que permite, además de visualizar que vías metabólicas presentan una mayor evidencia de estar diferencialmente expresadas, identificar las conexiones entre genes que pertenecen a más de una vía. Adicionalmente, si así se desea, también permite classificar, mediante una escala de color, aquellos genes que están sobrexpresados o infraexpresados.
En la Tabla 6 se muestra la summary table del control de calidad de los datos crudos realizado mediante arrayQualityMetrics(). En primer lugar, observamos que ningún array está marcado 3 veces, indicando que no existe ninguna muestra especialmente problemática y que la calidad global de nuestros datos es buena. Addicionalmente, si analizamos los resultados en detalle, identificamos que de los 27 arrays, 10 están marcados una sola vez y uno 2 veces. Mientras que los arrays marcados una vez no implican ningún problema para la normalización, el array marcado dos veces podría serlo y es posible que deba ser eliminado.
| array | sampleNames | 1 | 2 | 3 | Title | Group |
|---|---|---|---|---|---|---|
| 1 | FR.1 | 60% Fructose 1 | FR | |||
| 2 | FR.2 | 60% Fructose 2 | FR | |||
| 3 | FR.3 | X | 60% Fructose 3 | FR | ||
| 4 | AC.1 | X | X | Adjusted Calories 1 | AC | |
| 5 | AC.2 | Adjusted Calories 2 | AC | |||
| 6 | AC.3 | Adjusted Calories 3 | AC | |||
| 7 | CT.1 | AIN-93M Purified (Control) 1 | CT | |||
| 8 | CT.2 | AIN-93M Purified (Control) 2 | CT | |||
| 9 | CT.3 | AIN-93M Purified (Control) 3 | CT | |||
| 10 | AR.1 | X | Atherogenic Rodent 1 | AR | ||
| 11 | AR.2 | X | Atherogenic Rodent 2 | AR | ||
| 12 | AR.3 | X | Atherogenic Rodent 3 | AR | ||
| 13 | LAR.1 | Current LAR Diet 1 | LAR | |||
| 14 | LAR.2 | Current LAR Diet 2 | LAR | |||
| 15 | LAR.3 | Current LAR Diet 3 | LAR | |||
| 16 | DHA.1 | X | DHA-supplemented 1 | DHA | ||
| 17 | DHA.2 | DHA-supplemented 2 | DHA | |||
| 18 | DHA.3 | DHA-supplemented 3 | DHA | |||
| 19 | DR.1 | Diet-restriction 1 | DR | |||
| 20 | DR.2 | Diet-restriction 2 | DR | |||
| 21 | DR.3 | Diet-restriction 3 | DR | |||
| 22 | EFA.1 | X | EFA Deficient 1 | EFA | ||
| 23 | EFA.2 | X | EFA Deficient 2 | EFA | ||
| 24 | EFA.3 | X | EFA Deficient 3 | EFA | ||
| 25 | HF.1 | X | High Fat 1 | HF | ||
| 26 | HF.2 | X | High Fat 2 | HF | ||
| 27 | HF.3 | High Fat 3 | HF |
Tabla 6: contenido de la summary table (index.html) obtenida al aplicar la función arrayQualityMetrics() sobre los datos crudos (raw data).
Para complementar estos resultados y reforzar nuestra decisión respecto al array “problemático” (AC.1), nos hemos ayudado de un boxplot (Figura 1.A) y un PCA plot (Figura 1.B). Comparando este array con los de su mismo grupo (AC.2, AC.3), observamos que el patrón de intensidad del boxplot presenta diferencias y que su posición en el PCA plot dista considerablemente del resto. Esto refuerza la idea de que este array podría ser defectuoso y, por lo tanto, ha sido eliminado.
Figura 1: boxplot de los datos crudos (A). PCA plot de los datos crudos (B).
Una vez eliminado el array AC.1 y normalizados los datos, se ha realizado un segundo control de calidad para determinar si la normalización ha funcionado. En la Tabla 8 se muestra la tabla resumen del output de arrayQualityMetrics() mientras que en la Figura 2 se muestran un boxplot y un PCA plot. Por un lado, observamos que, como consecuencia de la normalización, el número de arrays marcados ha pasado de 11 a 2 y el número de marcas de 12 a 2. Esto indica que, efectivamente, la normalización ha funcionado. Por otro lado, tal y como se esperaba, observamos que los patrones de intensidad inter e intragrupales del boxplot son ahora mucho más homogenéos (Figura 2.A). Finalmente, en contraste con lo que observábamos para los datos crudos, el PCA plot muestra una agrupación mucho más palpable entre los chips del mismo grupo (Figura 2.B). Además, sugiere la pertinencia o no al grupo DR es la principal fuente de variabilidad (PC1 = 21.4%). En cuanto a la PC2 (14%), identificamos una considerable diferenciación entre el grupo AR y el resto de grupos.
| array | sampleNames | 1 | 2 | 3 | Title | Group |
|---|---|---|---|---|---|---|
| 1 | FR.1 | 60% Fructose 1 | FR | |||
| 2 | FR.2 | 60% Fructose 2 | FR | |||
| 3 | FR.3 | 60% Fructose 3 | FR | |||
| 4 | AC.1 | Adjusted Calories 1 | AC | |||
| 5 | AC.2 | Adjusted Calories 2 | AC | |||
| 6 | AC.3 | X | Adjusted Calories 3 | AC | ||
| 7 | CT.1 | AIN-93M Purified (Control) 1 | CT | |||
| 8 | CT.2 | AIN-93M Purified (Control) 2 | CT | |||
| 9 | CT.3 | AIN-93M Purified (Control) 3 | CT | |||
| 10 | AR.1 | Atherogenic Rodent 1 | AR | |||
| 11 | AR.2 | Atherogenic Rodent 2 | AR | |||
| 12 | AR.3 | Atherogenic Rodent 3 | AR | |||
| 13 | LAR.1 | Current LAR Diet 1 | LAR | |||
| 14 | LAR.2 | Current LAR Diet 2 | LAR | |||
| 15 | LAR.3 | Current LAR Diet 3 | LAR | |||
| 16 | DHA.1 | DHA-supplemented 1 | DHA | |||
| 17 | DHA.2 | DHA-supplemented 2 | DHA | |||
| 18 | DHA.3 | DHA-supplemented 3 | DHA | |||
| 19 | DR.1 | X | Diet-restriction 1 | DR | ||
| 20 | DR.2 | Diet-restriction 2 | DR | |||
| 21 | DR.3 | Diet-restriction 3 | DR | |||
| 22 | EFA.1 | EFA Deficient 1 | EFA | |||
| 23 | EFA.2 | EFA Deficient 2 | EFA | |||
| 24 | EFA.3 | EFA Deficient 3 | EFA | |||
| 25 | HF.1 | High Fat 1 | HF | |||
| 26 | HF.2 | High Fat 2 | HF | |||
| 27 | HF.3 | High Fat 3 | HF |
Tabla 8: contenido de la summary table (index.html) obtenida al aplicar la función arrayQualityMetrics() sobre los datos normalizados (normalized data).
Figura 2: boxplot de los datos normalizados (A). PCA plot de los datos normalizados (B).
Préviamente a la identificación de los genes diferencialmente expresados en cada comparación, se ha realizado un filtrado inespecífico con el objetivo de eliminar aquellos genes con una menor probabilidad de presentar diferencias. La Figura 3 contiene dos SD plots que muestran la desviación estándar total (calculada a partir de todos los arrays) de cada uno de los genes frente a su índice en función de esta variabilidad. Si centramos nuestra atención en el SD plot generado antes del filtrado (Figura 3.A), observamos que de los casi 50000 genes, un 85% tiene una variación total pequeña (sd < 0.25) y similar. Esto avala la idea de que solo la expresión de unos pocos genes varía entre condiciones experimentales y nos permite fijar el threshold para el filtrado (0.8). En contraposición, si observamos el SD plot generado después del filtrado, observamos que de los 3100 genes que quedan, la variabilidad es superior y no tan constante (Figura 3.B).
Figura 3: SD plot de los datos normalizados (A). SD plot de los datos normalizados y filtrados (B).
Una vez filtrados los genes y establecidas las comparaciones (Tabla 5), identificaremos que genes estan diferencialmente expresados en cada una de ellas. A continuación se muestran, para cada una de las 8 dietas, los 75 genes que presentan una mayor evidencia de estar diferencialmente expresados respecto al control (Tablas 9-16).
Control vs 60% Fructose (CTvsFR):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 848 | 1425314_at | Adgrv1 | 110789 | adhesion G protein-coupled receptor V1 | -1.75 | 6.31 | -7.06 | 3.3e-07 | 1.0e-03 | 6.59 |
| 645 | 1423130_a_at | Srsf5 | 20384 | serine/arginine-rich splicing factor 5 | -1.43 | 9.62 | -6.41 | 1.5e-06 | 2.3e-03 | 5.23 |
| 423 | 1419568_at | Mapk1 | 26413 | mitogen-activated protein kinase 1 | -1.15 | 6.08 | -5.68 | 8.6e-06 | 8.8e-03 | 3.66 |
| 356 | 1418858_at | Aox3 | 71724 | aldehyde oxidase 3 | -1.51 | 11.36 | -5.33 | 2.0e-05 | 1.2e-02 | 2.86 |
| 1486 | 1434677_at | Hps5 | 246694 | HPS5, biogenesis of lysosomal organelles complex 2 subunit 2 | -0.93 | 4.47 | -5.36 | 1.9e-05 | 1.2e-02 | 2.94 |
| 2116 | 1443825_x_at | Spaca3 | 75622 | sperm acrosome associated 3 | 0.81 | 4.16 | 5.20 | 2.8e-05 | 1.2e-02 | 2.56 |
| 2810 | 1455387_at | Nufip2 | 68564 | nuclear fragile X mental retardation protein interacting protein 2 | -1.00 | 7.17 | -5.25 | 2.5e-05 | 1.2e-02 | 2.69 |
| 185 | 1417409_at | Jun | 16476 | jun proto-oncogene | -2.15 | 6.97 | -5.07 | 3.9e-05 | 1.4e-02 | 2.27 |
| 763 | 1424504_at | Rab22a | 19334 | RAB22A, member RAS oncogene family | 0.96 | 5.69 | 5.02 | 4.4e-05 | 1.4e-02 | 2.16 |
| 1396 | 1433888_at | Atp2b2 | 11941 | ATPase, Ca++ transporting, plasma membrane 2 | 1.79 | 4.36 | 4.97 | 4.9e-05 | 1.4e-02 | 2.06 |
| 2235 | 1448136_at | Enpp2 | 18606 | ectonucleotide pyrophosphatase/phosphodiesterase 2 | -0.85 | 8.66 | -5.01 | 4.5e-05 | 1.4e-02 | 2.14 |
| 381 | 1419147_at | Rec8 | 56739 | REC8 meiotic recombination protein | 0.87 | 4.58 | 4.79 | 7.7e-05 | 1.5e-02 | 1.65 |
| 1429 | 1434188_at | Slc16a12 | 240638 | solute carrier family 16 (monocarboxylic acid transporters), member 12 | -0.85 | 7.51 | -4.86 | 6.6e-05 | 1.5e-02 | 1.80 |
| 1954 | 1439795_at | Adgrg2 | 237175 | adhesion G protein-coupled receptor G2 | -0.82 | 3.24 | -4.78 | 8.0e-05 | 1.5e-02 | 1.61 |
| 2339 | 1449248_at | Clcn2 | 12724 | chloride channel, voltage-sensitive 2 | -0.88 | 6.39 | -4.79 | 7.7e-05 | 1.5e-02 | 1.65 |
| 3049 | 1460318_at | Csrp3 | 13009 | cysteine and glycine-rich protein 3 | -0.98 | 8.29 | -4.85 | 6.7e-05 | 1.5e-02 | 1.78 |
| 485 | 1420630_at | Fam234b | 74525 | family with sequence similarity 234, member B | -0.68 | 7.05 | -4.61 | 1.2e-04 | 2.2e-02 | 1.23 |
| 2056 | 1441992_at | Rab14 | 68365 | RAB14, member RAS oncogene family | -1.39 | 5.84 | -4.57 | 1.3e-04 | 2.3e-02 | 1.14 |
| 361 | 1418940_at | Sult1b1 | 56362 | sulfotransferase family 1B, member 1 | -0.72 | 7.93 | -4.43 | 1.9e-04 | 2.7e-02 | 0.82 |
| 371 | 1419042_at | Iigp1 | 60440 | interferon inducible GTPase 1 | -0.75 | 11.15 | -4.41 | 2.0e-04 | 2.7e-02 | 0.76 |
| 570 | 1421977_at | Mmp19 | 58223 | matrix metallopeptidase 19 | -0.80 | 5.73 | -4.46 | 1.8e-04 | 2.7e-02 | 0.89 |
| 889 | 1425774_at | Srrm4 | 68955 | serine/arginine repetitive matrix 4 | -0.76 | 4.33 | -4.42 | 2.0e-04 | 2.7e-02 | 0.78 |
| 2730 | 1454685_at | Gpr146 | 80290 | G protein-coupled receptor 146 | -0.93 | 8.09 | -4.47 | 1.7e-04 | 2.7e-02 | 0.90 |
| 2602 | 1452378_at | Malat1 | 72289 | metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) | -1.35 | 6.41 | -4.32 | 2.5e-04 | 3.2e-02 | 0.56 |
| 286 | 1418265_s_at | Irf2 | 16363 | interferon regulatory factor 2 | -0.73 | 8.11 | -4.29 | 2.7e-04 | 3.2e-02 | 0.49 |
| 404 | 1419430_at | Cyp26a1 | 13082 | cytochrome P450, family 26, subfamily a, polypeptide 1 | 2.24 | 8.44 | 4.29 | 2.7e-04 | 3.2e-02 | 0.48 |
| 806 | 1424861_at | D930016D06Rik | 100662 | RIKEN cDNA D930016D06 gene | -0.97 | 5.79 | -4.26 | 2.9e-04 | 3.3e-02 | 0.42 |
| 711 | 1423891_at | Gstt3 | 103140 | glutathione S-transferase, theta 3 | 0.88 | 8.69 | 4.23 | 3.1e-04 | 3.4e-02 | 0.36 |
| 2879 | 1456074_at | Sdr9c7 | 70061 | 4short chain dehydrogenase/reductase family 9C, member 7 | -0.73 | 7.22 | -4.21 | 3.3e-04 | 3.5e-02 | 0.32 |
| 910 | 1426153_a_at | Dsg2 | 13511 | desmoglein 2 | -0.91 | 3.74 | -4.17 | 3.7e-04 | 3.8e-02 | 0.21 |
| 1782 | 1437638_at | Srrm2 | 75956 | serine/arginine repetitive matrix 2 | -1.02 | 6.57 | -4.13 | 4.1e-04 | 3.9e-02 | 0.12 |
| 1856 | 1438459_x_at | Sfpq | 71514 | splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated) | -0.97 | 6.01 | -4.13 | 4.0e-04 | 3.9e-02 | 0.13 |
| 216 | 1417769_at | Psmc6 | 67089 | proteasome (prosome, macropain) 26S subunit, ATPase, 6 | -0.98 | 6.20 | -4.10 | 4.3e-04 | 3.9e-02 | 0.06 |
| 2441 | 1450788_at | Saa1 | 20208 | serum amyloid A 1 | -2.87 | 10.70 | -4.11 | 4.2e-04 | 3.9e-02 | 0.08 |
| 2633 | 1452766_at | Tppp | 72948 | tubulin polymerization promoting protein | -0.94 | 4.50 | -4.08 | 4.5e-04 | 4.0e-02 | 0.02 |
| 633 | 1422917_at | Epha1 | 13835 | Eph receptor A1 | -0.89 | 6.24 | -4.06 | 4.8e-04 | 4.1e-02 | -0.03 |
| 215 | 1417761_at | Apoa4 | 11808 | apolipoprotein A-IV | 1.32 | 10.92 | 4.05 | 4.9e-04 | 4.1e-02 | -0.06 |
| 2118 | 1443857_at | Hook3 | 320191 | hook microtubule tethering protein 3 | -0.74 | 5.14 | -4.01 | 5.4e-04 | 4.4e-02 | -0.15 |
| 1500 | 1434826_at | Rfesd | 218341 | Rieske (Fe-S) domain containing | -0.65 | 6.21 | -3.94 | 6.5e-04 | 5.1e-02 | -0.32 |
| 1713 | 1436934_s_at | Aco2 | 11429 | aconitase 2, mitochondrial | 0.54 | 9.69 | 3.93 | 6.6e-04 | 5.1e-02 | -0.32 |
| 868 | 1425514_at | Pik3r1 | 18708 | phosphoinositide-3-kinase regulatory subunit 1 | -1.15 | 6.74 | -3.92 | 6.9e-04 | 5.2e-02 | -0.36 |
| 151 | 1417126_a_at | Rpl22l1 | 68028 | ribosomal protein L22 like 1 | -0.68 | 10.60 | -3.88 | 7.5e-04 | 5.5e-02 | -0.44 |
| 2062 | 1442097_at | Gm32461 | 102635020 | predicted gene, 32461 | -0.95 | 6.58 | -3.86 | 7.9e-04 | 5.6e-02 | -0.49 |
| 2461 | 1450966_at | Crot | 74114 | carnitine O-octanoyltransferase | -0.68 | 11.88 | -3.85 | 8.0e-04 | 5.6e-02 | -0.50 |
| 1062 | 1427982_s_at | Syne2 | 319565 | spectrin repeat containing, nuclear envelope 2 | -0.84 | 5.87 | -3.83 | 8.5e-04 | 5.7e-02 | -0.55 |
| 1134 | 1428739_at | Enho | 69638 | energy homeostasis associated | -1.93 | 7.32 | -3.83 | 8.5e-04 | 5.7e-02 | -0.56 |
| 1294 | 1431101_a_at | Srd5a1 | 78925 | steroid 5 alpha-reductase 1 | 0.70 | 7.92 | 3.82 | 8.8e-04 | 5.8e-02 | -0.59 |
| 221 | 1417791_a_at | Zfp638 | 18139 | zinc finger protein 638 | -0.66 | 7.13 | -3.79 | 9.4e-04 | 5.8e-02 | -0.65 |
| 1395 | 1433884_at | Syt1 | 20979 | synaptotagmin I | -0.67 | 6.60 | -3.79 | 9.5e-04 | 5.8e-02 | -0.65 |
| 1450 | 1434401_at | Zcchc2 | 227449 | zinc finger, CCHC domain containing 2 | -0.72 | 7.75 | -3.80 | 9.1e-04 | 5.8e-02 | -0.62 |
| 2616 | 1452504_s_at | Ctbs | 74245 | chitobiase | -0.73 | 6.16 | -3.78 | 9.7e-04 | 5.8e-02 | -0.67 |
| 259 | 1418069_at | Apoc2 | 11813 | apolipoprotein C-II | 0.67 | 12.31 | 3.76 | 1.0e-03 | 5.9e-02 | -0.71 |
| 1243 | 1430037_at | Snx27 | 76742 | sorting nexin family member 27 | -0.63 | 5.35 | -3.73 | 1.1e-03 | 6.0e-02 | -0.78 |
| 1759 | 1437395_at | Tut4 | 230594 | terminal uridylyl transferase 4 | -0.58 | 7.05 | -3.75 | 1.0e-03 | 6.0e-02 | -0.74 |
| 2150 | 1444437_at | Usp34 | 17847 | ubiquitin specific peptidase 34 | -0.94 | 3.95 | -3.74 | 1.1e-03 | 6.0e-02 | -0.77 |
| 2451 | 1450876_at | Cfh | 12628 | complement component factor h | -0.68 | 10.69 | -3.75 | 1.0e-03 | 6.0e-02 | -0.75 |
| 91 | 1416639_at | Slc2a5 | 56485 | solute carrier family 2 (facilitated glucose transporter), member 5 | 0.70 | 5.74 | 3.71 | 1.1e-03 | 6.0e-02 | -0.83 |
| 518 | 1421011_at | Hsd17b11 | 114664 | hydroxysteroid (17-beta) dehydrogenase 11 | -0.77 | 7.87 | -3.71 | 1.1e-03 | 6.0e-02 | -0.82 |
| 2253 | 1448328_at | Sh3bp2 | 24055 | SH3-domain binding protein 2 | -0.86 | 6.63 | -3.72 | 1.1e-03 | 6.0e-02 | -0.80 |
| 196 | 1417586_at | Timeless | 21853 | timeless circadian clock 1 | -0.68 | 4.51 | -3.65 | 1.3e-03 | 6.0e-02 | -0.96 |
| 695 | 1423693_at | Cela1 | 109901 | chymotrypsin-like elastase family, member 1 | -0.82 | 9.17 | -3.66 | 1.3e-03 | 6.0e-02 | -0.93 |
| 798 | 1424770_at | Cald1 | 109624 | caldesmon 1 | 0.83 | 10.22 | 3.65 | 1.3e-03 | 6.0e-02 | -0.95 |
| 1855 | 1438450_at | Lin7a | 108030 | lin-7 homolog A (C. elegans) | -0.64 | 6.69 | -3.70 | 1.2e-03 | 6.0e-02 | -0.86 |
| 1873 | 1438658_a_at | S1pr3 | 13610 | sphingosine-1-phosphate receptor 3 | 0.87 | 5.98 | 3.67 | 1.3e-03 | 6.0e-02 | -0.93 |
| 2086 | 1442612_at | C730036E19Rik | 402734 | RIKEN cDNA C730036E19 gene | -1.07 | 5.71 | -3.66 | 1.3e-03 | 6.0e-02 | -0.94 |
| 2640 | 1452864_at | Med12l | 329650 | mediator complex subunit 12-like | -0.59 | 4.80 | -3.68 | 1.2e-03 | 6.0e-02 | -0.90 |
| 2888 | 1456169_at | Tstd1 | 226654 | thiosulfate sulfurtransferase (rhodanese)-like domain containing 1 | -0.85 | 7.91 | -3.69 | 1.2e-03 | 6.0e-02 | -0.88 |
| 394 | 1419319_at | Saa4 | 20211 | serum amyloid A 4 | -1.34 | 7.49 | -3.64 | 1.4e-03 | 6.1e-02 | -0.99 |
| 1002 | 1427171_at | Rlf | 109263 | rearranged L-myc fusion sequence | -0.91 | 6.52 | -3.63 | 1.4e-03 | 6.1e-02 | -1.01 |
| 3029 | 1460044_at | Onecut2 | 225631 | one cut domain, family member 2 | -0.79 | 8.43 | -3.63 | 1.4e-03 | 6.1e-02 | -1.00 |
| 125 | 1416930_at | Ly6d | 17068 | lymphocyte antigen 6 complex, locus D | 1.11 | 5.75 | 3.60 | 1.5e-03 | 6.3e-02 | -1.07 |
| 1278 | 1430693_at | Pnpla5 | 75772 | patatin-like phospholipase domain containing 5 | 1.69 | 5.30 | 3.60 | 1.5e-03 | 6.3e-02 | -1.07 |
| 2019 | 1440921_at | Nlrp12 | 378425 | NLR family, pyrin domain containing 12 | -1.24 | 8.48 | -3.61 | 1.5e-03 | 6.3e-02 | -1.06 |
| 2835 | 1455621_at | Zfp870 | 240066 | zinc finger protein 870 | -0.76 | 3.91 | -3.60 | 1.5e-03 | 6.3e-02 | -1.08 |
| 637 | 1422964_at | Rad23a | 19358 | RAD23 homolog A, nucleotide excision repair protein | 0.61 | 6.79 | 3.59 | 1.5e-03 | 6.3e-02 | -1.10 |
Tabla 9: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta FR.
Control vs Adjusted Calories Diet (CTvsAC):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 236 | 1417867_at | Cfd | 11537 | complement factor D (adipsin) | 5.57 | 4.94 | 13.58 | 1.7e-12 | 2.6e-09 | 18.36 |
| 702 | 1423804_a_at | Idi1 | 319554 | isopentenyl-diphosphate delta isomerase | -4.15 | 8.97 | -13.87 | 1.1e-12 | 2.6e-09 | 18.76 |
| 598 | 1422533_at | Cyp51 | 13121 | cytochrome P450, family 51 | -3.22 | 7.93 | -12.78 | 5.9e-12 | 6.0e-09 | 17.22 |
| 24 | 1415993_at | Sqle | 20775 | squalene epoxidase | -4.83 | 8.48 | -12.32 | 1.2e-11 | 9.4e-09 | 16.55 |
| 640 | 1423078_a_at | Msmo1 | 66234 | methylsterol monoxygenase 1 | -2.58 | 9.92 | -11.73 | 3.3e-11 | 2.0e-08 | 15.62 |
| 1009 | 1427229_at | Hmgcr | 15357 | 3-hydroxy-3-methylglutaryl-Coenzyme A reductase | -2.86 | 7.27 | -10.02 | 7.0e-10 | 3.6e-07 | 12.74 |
| 2234 | 1448130_at | Fdft1 | 14137 | farnesyl diphosphate farnesyl transferase 1 | -2.14 | 9.10 | -9.36 | 2.5e-09 | 1.1e-06 | 11.52 |
| 675 | 1423418_at | Fdps | 110196 | farnesyl diphosphate synthetase | -2.56 | 10.09 | -8.27 | 2.3e-08 | 7.9e-06 | 9.37 |
| 826 | 1425028_a_at | Tpm2 | 22004 | tropomyosin 2, beta | 2.26 | 6.18 | 8.30 | 2.2e-08 | 7.9e-06 | 9.43 |
| 26 | 1416022_at | Fabp5 | 16592 | fatty acid binding protein 5, epidermal | -4.48 | 8.60 | -7.96 | 4.5e-08 | 1.2e-05 | 8.72 |
| 49 | 1416222_at | Nsdhl | 18194 | NAD(P) dependent steroid dehydrogenase-like | -1.90 | 9.21 | -8.01 | 4.1e-08 | 1.2e-05 | 8.82 |
| 1051 | 1427893_a_at | Pmvk | 68603 | phosphomevalonate kinase | -1.91 | 8.39 | -7.94 | 4.7e-08 | 1.2e-05 | 8.69 |
| 2708 | 1454067_a_at | 4931406C07Rik | 70984 | RIKEN cDNA 4931406C07 gene | 1.59 | 9.72 | 7.65 | 8.8e-08 | 2.1e-05 | 8.08 |
| 2748 | 1454838_s_at | Pkdcc | 106522 | protein kinase domain containing, cytoplasmic | -1.44 | 7.22 | -7.42 | 1.5e-07 | 3.3e-05 | 7.56 |
| 3 | 1415776_at | Aldh3a2 | 11671 | aldehyde dehydrogenase family 3, subfamily A2 | 1.80 | 9.67 | 7.17 | 2.6e-07 | 5.3e-05 | 7.03 |
| 1764 | 1437453_s_at | Pcsk9 | 100102 | proprotein convertase subtilisin/kexin type 9 | -2.01 | 6.84 | -6.98 | 4.0e-07 | 7.6e-05 | 6.61 |
| 2287 | 1448619_at | Dhcr7 | 13360 | 7-dehydrocholesterol reductase | -1.98 | 9.64 | -6.89 | 4.9e-07 | 8.8e-05 | 6.41 |
| 2506 | 1451461_a_at | Aldoc | 11676 | aldolase C, fructose-bisphosphate | -1.60 | 7.85 | -6.84 | 5.5e-07 | 9.4e-05 | 6.29 |
| 588 | 1422438_at | Ephx1 | 13849 | epoxide hydrolase 1, microsomal | 1.37 | 11.05 | 6.73 | 7.1e-07 | 1.1e-04 | 6.05 |
| 2539 | 1451799_at | Ccdc25 | 67179 | coiled-coil domain containing 25 | -2.27 | 4.79 | -6.64 | 8.8e-07 | 1.4e-04 | 5.83 |
| 2292 | 1448663_s_at | Mvd | 192156 | mevalonate (diphospho) decarboxylase | -2.14 | 6.81 | -6.60 | 9.6e-07 | 1.4e-04 | 5.75 |
| 2260 | 1448382_at | Ehhadh | 74147 | enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase | 1.40 | 10.95 | 6.52 | 1.2e-06 | 1.6e-04 | 5.55 |
| 1259 | 1430401_at | 3110045C21Rik | 67303 | RIKEN cDNA 3110045C21 gene | -1.49 | 5.53 | -6.37 | 1.6e-06 | 2.2e-04 | 5.22 |
| 151 | 1417126_a_at | Rpl22l1 | 68028 | ribosomal protein L22 like 1 | -1.22 | 10.60 | -6.22 | 2.4e-06 | 3.0e-04 | 4.87 |
| 292 | 1418320_at | Prss8 | 76560 | protease, serine 8 (prostasin) | -2.06 | 5.24 | -6.16 | 2.7e-06 | 3.3e-04 | 4.73 |
| 928 | 1426452_a_at | Rab30 | 75985 | RAB30, member RAS oncogene family | 1.31 | 5.64 | 6.13 | 2.9e-06 | 3.4e-04 | 4.67 |
| 398 | 1419393_at | Abcg5 | 27409 | ATP binding cassette subfamily G member 5 | 1.55 | 9.43 | 6.10 | 3.1e-06 | 3.6e-04 | 4.59 |
| 3033 | 1460118_at | Pde5a | 242202 | phosphodiesterase 5A, cGMP-specific | 1.42 | 4.34 | 6.03 | 3.7e-06 | 4.1e-04 | 4.42 |
| 1944 | 1439560_x_at | Smim22 | 432995 | small integral membrane protein 22 | -1.25 | 7.63 | -5.92 | 4.9e-06 | 5.2e-04 | 4.16 |
| 339 | 1418760_at | Rdh11 | 17252 | retinol dehydrogenase 11 | -1.90 | 8.71 | -5.72 | 7.9e-06 | 8.1e-04 | 3.68 |
| 323 | 1418604_at | Avpr1a | 54140 | arginine vasopressin receptor 1A | -1.50 | 6.77 | -5.64 | 9.6e-06 | 9.3e-04 | 3.49 |
| 1926 | 1439397_at | Fmn1 | 14260 | formin 1 | -1.60 | 5.35 | -5.65 | 9.4e-06 | 9.3e-04 | 3.52 |
| 545 | 1421410_a_at | Pstpip2 | 19201 | proline-serine-threonine phosphatase-interacting protein 2 | -1.59 | 6.86 | -5.59 | 1.1e-05 | 9.6e-04 | 3.40 |
| 591 | 1422474_at | Pde4b | 18578 | phosphodiesterase 4B, cAMP specific | -1.41 | 6.78 | -5.60 | 1.0e-05 | 9.6e-04 | 3.41 |
| 3072 | 1460684_at | Tm7sf2 | 73166 | transmembrane 7 superfamily member 2 | -1.17 | 10.46 | -5.49 | 1.4e-05 | 1.2e-03 | 3.13 |
| 592 | 1422479_at | Acss2 | 60525 | acyl-CoA synthetase short-chain family member 2 | -1.77 | 10.64 | -5.46 | 1.5e-05 | 1.3e-03 | 3.06 |
| 821 | 1424973_at | Cyp3a25 | 56388 | cytochrome P450, family 3, subfamily a, polypeptide 25 | 0.99 | 12.22 | 5.44 | 1.5e-05 | 1.3e-03 | 3.03 |
| 1893 | 1438992_x_at | Atf4 | 11911 | activating transcription factor 4 | -1.05 | 8.44 | -5.41 | 1.7e-05 | 1.3e-03 | 2.96 |
| 1226 | 1429642_at | Zfand4 | 67492 | zinc finger, AN1-type domain 4 | -1.25 | 8.11 | -5.40 | 1.7e-05 | 1.3e-03 | 2.93 |
| 1807 | 1437868_at | Tent5a | 212943 | terminal nucleotidyltransferase 5A | -1.52 | 7.03 | -5.31 | 2.2e-05 | 1.7e-03 | 2.71 |
| 305 | 1418438_at | Fabp2 | 14079 | fatty acid binding protein 2, intestinal | 1.12 | 10.57 | 5.26 | 2.4e-05 | 1.8e-03 | 2.59 |
| 478 | 1420515_a_at | Pglyrp2 | 57757 | peptidoglycan recognition protein 2 | -0.92 | 9.16 | -5.26 | 2.4e-05 | 1.8e-03 | 2.60 |
| 763 | 1424504_at | Rab22a | 19334 | RAB22A, member RAS oncogene family | 1.12 | 5.69 | 5.23 | 2.6e-05 | 1.8e-03 | 2.53 |
| 661 | 1423257_at | Cyp4a14 | 13119 | cytochrome P450, family 4, subfamily a, polypeptide 14 | 4.58 | 8.78 | 5.19 | 2.9e-05 | 1.9e-03 | 2.43 |
| 1067 | 1428022_at | Obp2a | 227627 | odorant binding protein 2A | 2.71 | 4.78 | 5.17 | 3.0e-05 | 1.9e-03 | 2.37 |
| 1171 | 1428988_at | Abcc3 | 76408 | ATP-binding cassette, sub-family C (CFTR/MRP), member 3 | 1.54 | 9.26 | 5.19 | 2.8e-05 | 1.9e-03 | 2.43 |
| 2026 | 1441098_at | Pnldc1 | 240023 | poly(A)-specific ribonuclease (PARN)-like domain containing 1 | 1.32 | 5.14 | 5.18 | 3.0e-05 | 1.9e-03 | 2.39 |
| 2116 | 1443825_x_at | Spaca3 | 75622 | sperm acrosome associated 3 | 0.90 | 4.16 | 5.17 | 3.0e-05 | 1.9e-03 | 2.38 |
| 2161 | 1444790_at | Hsbp1l1 | 66255 | heat shock factor binding protein 1-like 1 | -2.27 | 4.71 | -5.17 | 3.0e-05 | 1.9e-03 | 2.37 |
| 2551 | 1451903_at | Kynu | 70789 | kynureninase | -0.96 | 5.68 | -5.15 | 3.2e-05 | 2.0e-03 | 2.32 |
| 375 | 1419095_a_at | Apom | 55938 | apolipoprotein M | -0.84 | 12.21 | -5.11 | 3.5e-05 | 2.1e-03 | 2.23 |
| 489 | 1420656_at | Abcg8 | 67470 | ATP binding cassette subfamily G member 8 | 1.14 | 8.31 | 5.10 | 3.6e-05 | 2.1e-03 | 2.20 |
| 138 | 1417017_at | Cyp17a1 | 13074 | cytochrome P450, family 17, subfamily a, polypeptide 1 | -1.75 | 7.07 | -5.07 | 3.8e-05 | 2.2e-03 | 2.14 |
| 459 | 1420013_s_at | Lss | 16987 | lanosterol synthase | -1.52 | 8.16 | -5.06 | 4.0e-05 | 2.2e-03 | 2.10 |
| 2545 | 1451828_a_at | Acsl4 | 50790 | acyl-CoA synthetase long-chain family member 4 | -1.36 | 6.23 | -5.06 | 4.0e-05 | 2.2e-03 | 2.11 |
| 2728 | 1454671_at | Insig1 | 231070 | insulin induced gene 1 | -1.36 | 11.35 | -5.05 | 4.1e-05 | 2.3e-03 | 2.08 |
| 1756 | 1437341_x_at | Cnp | 12799 | 2’,3’-cyclic nucleotide 3’ phosphodiesterase | -1.09 | 8.70 | -4.99 | 4.7e-05 | 2.5e-03 | 1.94 |
| 701 | 1423797_at | Aacs | 78894 | acetoacetyl-CoA synthetase | -2.00 | 7.55 | -4.94 | 5.3e-05 | 2.8e-03 | 1.83 |
| 1649 | 1436404_at | Tlcd1 | 68385 | TLC domain containing 1 | -0.98 | 6.66 | -4.94 | 5.4e-05 | 2.8e-03 | 1.82 |
| 416 | 1419504_at | Mogat1 | 68393 | monoacylglycerol O-acyltransferase 1 | 1.56 | 4.51 | 4.92 | 5.7e-05 | 2.9e-03 | 1.76 |
| 1578 | 1435517_x_at | Ralb | 64143 | v-ral simian leukemia viral oncogene B | -1.01 | 6.52 | -4.91 | 5.8e-05 | 2.9e-03 | 1.74 |
| 1541 | 1435254_at | Plxnb1 | 235611 | plexin B1 | -1.39 | 6.63 | -4.89 | 6.1e-05 | 3.0e-03 | 1.69 |
| 1115 | 1428586_at | Tmem41b | 233724 | transmembrane protein 41B | -1.14 | 5.97 | -4.87 | 6.4e-05 | 3.1e-03 | 1.64 |
| 1698 | 1436838_x_at | Cotl1 | 72042 | coactosin-like 1 (Dictyostelium) | -1.24 | 7.86 | -4.86 | 6.5e-05 | 3.1e-03 | 1.63 |
| 2404 | 1450109_s_at | Abcc2 | 12780 | ATP-binding cassette, sub-family C (CFTR/MRP), member 2 | 0.87 | 10.30 | 4.83 | 7.1e-05 | 3.4e-03 | 1.54 |
| 203 | 1417695_a_at | Soat1 | 20652 | sterol O-acyltransferase 1 | -1.16 | 4.94 | -4.81 | 7.5e-05 | 3.5e-03 | 1.49 |
| 879 | 1425645_s_at | Cyp2b10 | 13088 | cytochrome P450, family 2, subfamily b, polypeptide 10 | 1.54 | 4.58 | 4.78 | 8.0e-05 | 3.6e-03 | 1.42 |
| 1830 | 1438169_a_at | Frmd4b | 232288 | FERM domain containing 4B | -1.17 | 10.28 | -4.77 | 8.2e-05 | 3.6e-03 | 1.40 |
| 1855 | 1438450_at | Lin7a | 108030 | lin-7 homolog A (C. elegans) | -0.92 | 6.69 | -4.76 | 8.4e-05 | 3.6e-03 | 1.38 |
| 2245 | 1448261_at | Cdh1 | 12550 | cadherin 1 | -1.33 | 9.05 | -4.76 | 8.4e-05 | 3.6e-03 | 1.38 |
| 2888 | 1456169_at | Tstd1 | 226654 | thiosulfate sulfurtransferase (rhodanese)-like domain containing 1 | -1.23 | 7.91 | -4.77 | 8.1e-05 | 3.6e-03 | 1.41 |
| 177 | 1417382_at | Entpd5 | 12499 | ectonucleoside triphosphate diphosphohydrolase 5 | 0.91 | 9.87 | 4.75 | 8.6e-05 | 3.7e-03 | 1.36 |
| 23 | 1415984_at | Acadm | 11364 | acyl-Coenzyme A dehydrogenase, medium chain | 0.83 | 11.76 | 4.73 | 8.9e-05 | 3.8e-03 | 1.32 |
| 936 | 1426526_s_at | Ovgp1 | 12659 | oviductal glycoprotein 1 | 1.00 | 3.50 | 4.72 | 9.3e-05 | 3.8e-03 | 1.28 |
| 2540 | 1451803_a_at | Vegfb | 22340 | vascular endothelial growth factor B | -0.88 | 6.60 | -4.72 | 9.3e-05 | 3.8e-03 | 1.28 |
Tabla 10: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta AC.
Control vs Atherogenic Rodent Diet (CTvsAR):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 2345 | 1449309_at | Cyp8b1 | 13124 | cytochrome P450, family 8, subfamily b, polypeptide 1 | -6.25 | 10.56 | -23.57 | 1.2e-17 | 3.6e-14 | 29.49 |
| 598 | 1422533_at | Cyp51 | 13121 | cytochrome P450, family 51 | -3.54 | 7.93 | -15.72 | 7.9e-14 | 1.2e-10 | 21.57 |
| 640 | 1423078_a_at | Msmo1 | 66234 | methylsterol monoxygenase 1 | -2.91 | 9.92 | -14.80 | 2.8e-13 | 2.9e-10 | 20.37 |
| 702 | 1423804_a_at | Idi1 | 319554 | isopentenyl-diphosphate delta isomerase | -3.79 | 8.97 | -14.16 | 7.1e-13 | 5.4e-10 | 19.50 |
| 24 | 1415993_at | Sqle | 20775 | squalene epoxidase | -4.56 | 8.48 | -13.01 | 4.1e-12 | 2.1e-09 | 17.82 |
| 398 | 1419393_at | Abcg5 | 27409 | ATP binding cassette subfamily G member 5 | 2.97 | 9.43 | 13.06 | 3.7e-12 | 2.1e-09 | 17.90 |
| 256 | 1418028_at | Dct | 13190 | dopachrome tautomerase | -3.46 | 7.51 | -12.80 | 5.6e-12 | 2.5e-09 | 17.50 |
| 675 | 1423418_at | Fdps | 110196 | farnesyl diphosphate synthetase | -3.52 | 10.09 | -12.70 | 6.6e-12 | 2.5e-09 | 17.35 |
| 489 | 1420656_at | Abcg8 | 67470 | ATP binding cassette subfamily G member 8 | 2.40 | 8.31 | 12.03 | 2.0e-11 | 6.8e-09 | 16.29 |
| 49 | 1416222_at | Nsdhl | 18194 | NAD(P) dependent steroid dehydrogenase-like | -2.49 | 9.21 | -11.76 | 3.1e-11 | 9.7e-09 | 15.84 |
| 588 | 1422438_at | Ephx1 | 13849 | epoxide hydrolase 1, microsomal | 1.87 | 11.05 | 10.24 | 4.6e-10 | 1.3e-07 | 13.20 |
| 547 | 1421430_at | Rad51b | 19363 | RAD51 paralog B | 3.06 | 4.15 | 10.04 | 6.8e-10 | 1.6e-07 | 12.83 |
| 3072 | 1460684_at | Tm7sf2 | 73166 | transmembrane 7 superfamily member 2 | -1.92 | 10.46 | -10.08 | 6.3e-10 | 1.6e-07 | 12.90 |
| 67 | 1416368_at | Gsta4 | 14860 | glutathione S-transferase, alpha 4 | 2.23 | 9.39 | 9.66 | 1.4e-09 | 3.1e-07 | 12.10 |
| 741 | 1424278_a_at | Birc5 | 11799 | baculoviral IAP repeat-containing 5 | 2.15 | 3.49 | 9.13 | 3.9e-09 | 7.7e-07 | 11.08 |
| 2287 | 1448619_at | Dhcr7 | 13360 | 7-dehydrocholesterol reductase | -2.35 | 9.64 | -9.13 | 4.0e-09 | 7.7e-07 | 11.07 |
| 2234 | 1448130_at | Fdft1 | 14137 | farnesyl diphosphate farnesyl transferase 1 | -1.85 | 9.10 | -9.04 | 4.7e-09 | 8.1e-07 | 10.91 |
| 2649 | 1452954_at | Ube2c | 68612 | ubiquitin-conjugating enzyme E2C | 1.71 | 3.89 | 9.04 | 4.7e-09 | 8.1e-07 | 10.91 |
| 709 | 1423859_a_at | Ptgds | 19215 | prostaglandin D2 synthase (brain) | 2.29 | 6.16 | 8.92 | 6.0e-09 | 9.7e-07 | 10.67 |
| 478 | 1420515_a_at | Pglyrp2 | 57757 | peptidoglycan recognition protein 2 | -1.38 | 9.16 | -8.82 | 7.5e-09 | 1.1e-06 | 10.45 |
| 959 | 1426817_at | Mki67 | 17345 | antigen identified by monoclonal antibody Ki 67 | 1.73 | 4.14 | 8.82 | 7.5e-09 | 1.1e-06 | 10.45 |
| 821 | 1424973_at | Cyp3a25 | 56388 | cytochrome P450, family 3, subfamily a, polypeptide 25 | 1.42 | 12.22 | 8.70 | 9.4e-09 | 1.3e-06 | 10.22 |
| 1051 | 1427893_a_at | Pmvk | 68603 | phosphomevalonate kinase | -1.88 | 8.39 | -8.71 | 9.3e-09 | 1.3e-06 | 10.24 |
| 1008 | 1427202_at | Etfbkmt | 320204 | electron transfer flavoprotein beta subunit lysine methyltransferase | 2.35 | 8.29 | 8.64 | 1.1e-08 | 1.4e-06 | 10.09 |
| 592 | 1422479_at | Acss2 | 60525 | acyl-CoA synthetase short-chain family member 2 | -2.50 | 10.64 | -8.61 | 1.2e-08 | 1.4e-06 | 10.02 |
| 444 | 1419759_at | Abcb1a | 18671 | ATP-binding cassette, sub-family B (MDR/TAP), member 1A | 1.49 | 4.77 | 8.58 | 1.2e-08 | 1.5e-06 | 9.96 |
| 2770 | 1455025_at | Paqr9 | 75552 | progestin and adipoQ receptor family member IX | -1.69 | 10.41 | -8.53 | 1.4e-08 | 1.5e-06 | 9.86 |
| 2292 | 1448663_s_at | Mvd | 192156 | mevalonate (diphospho) decarboxylase | -2.44 | 6.81 | -8.42 | 1.7e-08 | 1.9e-06 | 9.64 |
| 26 | 1416022_at | Fabp5 | 16592 | fatty acid binding protein 5, epidermal | -4.21 | 8.60 | -8.37 | 1.9e-08 | 2.0e-06 | 9.53 |
| 848 | 1425314_at | Adgrv1 | 110789 | adhesion G protein-coupled receptor V1 | -2.02 | 6.31 | -8.15 | 3.0e-08 | 3.1e-06 | 9.08 |
| 1067 | 1428022_at | Obp2a | 227627 | odorant binding protein 2A | 3.76 | 4.78 | 8.03 | 3.9e-08 | 3.9e-06 | 8.81 |
| 228 | 1417821_at | D17H6S56E-5 | 110956 | DNA segment, Chr 17, human D6S56E 5 | 1.77 | 4.17 | 7.82 | 6.2e-08 | 5.8e-06 | 8.35 |
| 1034 | 1427474_s_at | Gstm3 | 14864 | glutathione S-transferase, mu 3 | 2.21 | 9.62 | 7.83 | 6.1e-08 | 5.8e-06 | 8.37 |
| 2254 | 1448330_at | Gstm1 | 14862 | glutathione S-transferase, mu 1 | 1.54 | 11.76 | 7.78 | 6.7e-08 | 6.1e-06 | 8.27 |
| 3077 | 1460732_a_at | Ppl | 19041 | periplakin | 1.66 | 5.70 | 7.69 | 8.2e-08 | 7.2e-06 | 8.07 |
| 957 | 1426808_at | Lgals3 | 16854 | lectin, galactose binding, soluble 3 | 2.28 | 6.46 | 7.56 | 1.1e-07 | 9.3e-06 | 7.79 |
| 1334 | 1432282_a_at | Tlcd2 | 380712 | TLC domain containing 2 | -1.36 | 10.31 | -7.52 | 1.2e-07 | 9.8e-06 | 7.71 |
| 1009 | 1427229_at | Hmgcr | 15357 | 3-hydroxy-3-methylglutaryl-Coenzyme A reductase | -1.91 | 7.27 | -7.48 | 1.3e-07 | 1.0e-05 | 7.62 |
| 3004 | 1459141_at | 1810008I18Rik | 100503969 | RIKEN cDNA 1810008I18 gene | -2.36 | 9.51 | -7.48 | 1.3e-07 | 1.0e-05 | 7.62 |
| 835 | 1425120_x_at | Ifi27l2b | 217845 | interferon, alpha-inducible protein 27 like 2B | 1.54 | 6.44 | 7.46 | 1.4e-07 | 1.0e-05 | 7.57 |
| 695 | 1423693_at | Cela1 | 109901 | chymotrypsin-like elastase family, member 1 | -1.67 | 9.17 | -7.44 | 1.4e-07 | 1.1e-05 | 7.53 |
| 339 | 1418760_at | Rdh11 | 17252 | retinol dehydrogenase 11 | -2.19 | 8.71 | -7.33 | 1.8e-07 | 1.3e-05 | 7.29 |
| 1125 | 1428670_at | 2610305J24Rik | 100034733 | RIKEN cDNA 2610305J24 gene | 2.30 | 4.40 | 7.25 | 2.2e-07 | 1.6e-05 | 7.10 |
| 2334 | 1449164_at | Cd68 | 12514 | CD68 antigen | 1.97 | 5.37 | 7.19 | 2.5e-07 | 1.7e-05 | 6.97 |
| 138 | 1417017_at | Cyp17a1 | 13074 | cytochrome P450, family 17, subfamily a, polypeptide 1 | -2.20 | 7.07 | -7.12 | 2.9e-07 | 2.0e-05 | 6.81 |
| 550 | 1421525_a_at | Naip5 | 17951 | NLR family, apoptosis inhibitory protein 5 | 1.39 | 3.38 | 7.02 | 3.6e-07 | 2.3e-05 | 6.60 |
| 901 | 1425964_x_at | Hspb1 | 15507 | heat shock protein 1 | 1.60 | 8.40 | 7.02 | 3.6e-07 | 2.3e-05 | 6.59 |
| 2017 | 1440899_at | Fmo5 | 14263 | flavin containing monooxygenase 5 | 1.76 | 10.64 | 7.04 | 3.5e-07 | 2.3e-05 | 6.62 |
| 151 | 1417126_a_at | Rpl22l1 | 68028 | ribosomal protein L22 like 1 | -1.22 | 10.60 | -6.95 | 4.2e-07 | 2.7e-05 | 6.44 |
| 1643 | 1436293_x_at | Ildr2 | 100039795 | immunoglobulin-like domain containing receptor 2 | 1.87 | 7.86 | 6.94 | 4.4e-07 | 2.7e-05 | 6.40 |
| 2151 | 1444438_at | Cib3 | 234421 | calcium and integrin binding family member 3 | 1.66 | 5.00 | 6.75 | 6.7e-07 | 4.1e-05 | 5.97 |
| 1765 | 1437457_a_at | Mtpn | 14489 | myotrophin | 1.32 | 8.85 | 6.72 | 7.4e-07 | 4.4e-05 | 5.89 |
| 1136 | 1428758_at | Tmem86a | 67893 | transmembrane protein 86A | 1.51 | 7.37 | 6.70 | 7.7e-07 | 4.5e-05 | 5.84 |
| 749 | 1424351_at | Wfdc2 | 67701 | WAP four-disulfide core domain 2 | 1.42 | 7.13 | 6.63 | 9.0e-07 | 5.1e-05 | 5.69 |
| 1627 | 1436174_at | Atad2 | 70472 | ATPase family, AAA domain containing 2 | 1.32 | 4.55 | 6.60 | 9.6e-07 | 5.4e-05 | 5.62 |
| 459 | 1420013_s_at | Lss | 16987 | lanosterol synthase | -1.76 | 8.16 | -6.58 | 1.0e-06 | 5.5e-05 | 5.58 |
| 2193 | 1446769_at | Ttc39c | 72747 | tetratricopeptide repeat domain 39C | -1.51 | 7.90 | -6.57 | 1.0e-06 | 5.6e-05 | 5.55 |
| 404 | 1419430_at | Cyp26a1 | 13082 | cytochrome P450, family 26, subfamily a, polypeptide 1 | 3.42 | 8.44 | 6.54 | 1.1e-06 | 5.9e-05 | 5.48 |
| 165 | 1417266_at | Ccl6 | 20305 | chemokine (C-C motif) ligand 6 | 1.87 | 6.57 | 6.53 | 1.1e-06 | 5.9e-05 | 5.46 |
| 3037 | 1460196_at | Cbr1 | 12408 | carbonyl reductase 1 | 0.97 | 9.57 | 6.51 | 1.2e-06 | 6.1e-05 | 5.41 |
| 812 | 1424898_at | Slc10a1 | 20493 | solute carrier family 10 (sodium/bile acid cotransporter family), member 1 | -1.14 | 12.67 | -6.48 | 1.3e-06 | 6.4e-05 | 5.34 |
| 486 | 1420647_a_at | Krt8 | 16691 | keratin 8 | 1.33 | 10.87 | 6.46 | 1.3e-06 | 6.4e-05 | 5.30 |
| 2506 | 1451461_a_at | Aldoc | 11676 | aldolase C, fructose-bisphosphate | -1.36 | 7.85 | -6.46 | 1.3e-06 | 6.4e-05 | 5.30 |
| 2445 | 1450826_a_at | Saa3 | 20210 | serum amyloid A 3 | 2.97 | 7.55 | 6.41 | 1.5e-06 | 7.3e-05 | 5.17 |
| 774 | 1424607_a_at | Gm4354 | 100043316 | predicted gene 4354 | 1.72 | 8.90 | 6.39 | 1.6e-06 | 7.5e-05 | 5.13 |
| 106 | 1416795_at | Cryl1 | 68631 | crystallin, lambda 1 | 1.25 | 6.97 | 6.37 | 1.7e-06 | 7.7e-05 | 5.08 |
| 2852 | 1455820_x_at | Scarb1 | 20778 | scavenger receptor class B, member 1 | 1.16 | 10.35 | 6.36 | 1.7e-06 | 7.8e-05 | 5.06 |
| 769 | 1424588_at | Srgap3 | 259302 | SLIT-ROBO Rho GTPase activating protein 3 | -1.28 | 4.96 | -6.35 | 1.8e-06 | 7.9e-05 | 5.02 |
| 730 | 1424133_at | Tmem98 | 103743 | transmembrane protein 98 | 1.03 | 7.01 | 6.33 | 1.8e-06 | 8.1e-05 | 4.98 |
| 186 | 1417420_at | Ccnd1 | 12443 | cyclin D1 | 1.66 | 6.87 | 6.28 | 2.1e-06 | 8.8e-05 | 4.86 |
| 520 | 1421040_a_at | Gsta2 | 14858 | glutathione S-transferase, alpha 2 (Yc2) | 2.44 | 10.11 | 6.27 | 2.1e-06 | 8.8e-05 | 4.85 |
| 1285 | 1430893_at | Mup10 | 100039008 | major urinary protein 10 | -1.99 | 9.35 | -6.27 | 2.1e-06 | 8.8e-05 | 4.85 |
| 3045 | 1460258_at | Cnmd | 16840 | chondromodulin | -1.60 | 6.31 | -6.28 | 2.0e-06 | 8.8e-05 | 4.87 |
| 2456 | 1450920_at | Ccnb2 | 12442 | cyclin B2 | 1.78 | 3.69 | 6.24 | 2.2e-06 | 9.2e-05 | 4.79 |
| 16 | 1415904_at | Lpl | 16956 | lipoprotein lipase | 2.06 | 8.79 | 6.20 | 2.5e-06 | 9.9e-05 | 4.69 |
Tabla 11: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta AR.
Control vs DHA-suplemented Diet (CTvsDHA):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 429 | 1419603_at | Ifi204 | 15951 | interferon activated gene 204 | -0.92 | 4.16 | -5.12 | 3.4e-05 | 7.7e-02 | 2.28 |
| 620 | 1422804_at | Serpinb6b | 20708 | serine (or cysteine) peptidase inhibitor, clade B, member 6b | -1.01 | 5.06 | -4.29 | 2.7e-04 | 7.7e-02 | 0.47 |
| 848 | 1425314_at | Adgrv1 | 110789 | adhesion G protein-coupled receptor V1 | -1.13 | 6.31 | -4.57 | 1.4e-04 | 7.7e-02 | 1.08 |
| 1158 | 1428877_at | Srp72 | 66661 | signal recognition particle 72 | 0.99 | 9.65 | 4.49 | 1.7e-04 | 7.7e-02 | 0.91 |
| 1198 | 1429262_at | Rassf6 | 73246 | Ras association (RalGDS/AF-6) domain family member 6 | -0.85 | 6.54 | -4.20 | 3.4e-04 | 7.7e-02 | 0.29 |
| 1287 | 1430981_s_at | Gpbp1 | 73274 | GC-rich promoter binding protein 1 | -1.11 | 6.93 | -4.30 | 2.6e-04 | 7.7e-02 | 0.50 |
| 1544 | 1435280_at | Pde4d | 238871 | phosphodiesterase 4D, cAMP specific | -1.27 | 5.20 | -4.48 | 1.7e-04 | 7.7e-02 | 0.89 |
| 1693 | 1436775_a_at | Ankrd17 | 81702 | ankyrin repeat domain 17 | 0.87 | 7.57 | 4.24 | 3.0e-04 | 7.7e-02 | 0.38 |
| 1840 | 1438242_at | Usp40 | 227334 | ubiquitin specific peptidase 40 | 0.74 | 5.88 | 4.24 | 3.0e-04 | 7.7e-02 | 0.38 |
| 2118 | 1443857_at | Hook3 | 320191 | hook microtubule tethering protein 3 | -0.78 | 5.14 | -4.19 | 3.5e-04 | 7.7e-02 | 0.25 |
| 2149 | 1444435_at | Vps13b | 666173 | vacuolar protein sorting 13B | 1.19 | 5.48 | 4.47 | 1.7e-04 | 7.7e-02 | 0.86 |
| 2457 | 1450932_s_at | Dock9 | 105445 | dedicator of cytokinesis 9 | -0.79 | 5.98 | -4.47 | 1.7e-04 | 7.7e-02 | 0.87 |
| 2731 | 1454699_at | Sesn1 | 140742 | sestrin 1 | -0.84 | 5.91 | -4.22 | 3.2e-04 | 7.7e-02 | 0.32 |
| 3019 | 1459894_at | Iqgap2 | 544963 | IQ motif containing GTPase activating protein 2 | 0.84 | 10.17 | 4.22 | 3.2e-04 | 7.7e-02 | 0.33 |
| 1009 | 1427229_at | Hmgcr | 15357 | 3-hydroxy-3-methylglutaryl-Coenzyme A reductase | -1.03 | 7.27 | -4.05 | 4.9e-04 | 9.5e-02 | -0.05 |
| 1078 | 1428171_at | Prpf39 | 328110 | pre-mRNA processing factor 39 | -1.14 | 5.77 | -4.02 | 5.3e-04 | 9.5e-02 | -0.10 |
| 2532 | 1451735_at | Arfrp1 | 76688 | ADP-ribosylation factor related protein 1 | -0.71 | 4.63 | -4.02 | 5.3e-04 | 9.5e-02 | -0.10 |
| 234 | 1417852_x_at | Clca3a1 | 12722 | chloride channel accessory 3A1 | -1.19 | 5.63 | -3.89 | 7.3e-04 | 1.0e-01 | -0.40 |
| 566 | 1421905_at | Tgs1 | 116940 | trimethylguanosine synthase 1 | 0.84 | 5.00 | 3.93 | 6.7e-04 | 1.0e-01 | -0.32 |
| 782 | 1424658_at | Taok1 | 216965 | TAO kinase 1 | -0.80 | 4.36 | -3.94 | 6.5e-04 | 1.0e-01 | -0.28 |
| 790 | 1424706_at | Zfp51 | 22709 | zinc finger protein 51 | -0.86 | 4.94 | -3.90 | 7.2e-04 | 1.0e-01 | -0.38 |
| 1460 | 1434449_at | Aqp4 | 11829 | aquaporin 4 | -1.31 | 4.93 | -3.97 | 6.0e-04 | 1.0e-01 | -0.22 |
| 1486 | 1434677_at | Hps5 | 246694 | HPS5, biogenesis of lysosomal organelles complex 2 subunit 2 | -0.66 | 4.47 | -3.83 | 8.6e-04 | 1.1e-01 | -0.53 |
| 2005 | 1440739_at | Vegfc | 22341 | vascular endothelial growth factor C | -0.67 | 5.75 | -3.83 | 8.4e-04 | 1.1e-01 | -0.52 |
| 2183 | 1446258_at | 9530067D14Rik | 100101632 | Riken cDNA 9530067D14 gene | 0.85 | 6.00 | 3.85 | 8.1e-04 | 1.1e-01 | -0.48 |
| 340 | 1418762_at | Cd55 | 13136 | CD55 molecule, decay accelerating factor for complement | -0.93 | 5.27 | -3.75 | 1.0e-03 | 1.1e-01 | -0.69 |
| 423 | 1419568_at | Mapk1 | 26413 | mitogen-activated protein kinase 1 | -0.75 | 6.08 | -3.73 | 1.1e-03 | 1.1e-01 | -0.74 |
| 763 | 1424504_at | Rab22a | 19334 | RAB22A, member RAS oncogene family | 0.72 | 5.69 | 3.77 | 9.9e-04 | 1.1e-01 | -0.65 |
| 1797 | 1437751_at | Ppargc1a | 19017 | peroxisome proliferative activated receptor, gamma, coactivator 1 alpha | -1.01 | 5.57 | -3.69 | 1.2e-03 | 1.1e-01 | -0.82 |
| 1905 | 1439108_at | Kmt2e | 69188 | lysine (K)-specific methyltransferase 2E | 0.93 | 7.27 | 3.69 | 1.2e-03 | 1.1e-01 | -0.82 |
| 2327 | 1449080_at | Hdac2 | 15182 | histone deacetylase 2 | -0.80 | 6.24 | -3.69 | 1.2e-03 | 1.1e-01 | -0.82 |
| 2431 | 1450715_at | Cyp1a2 | 13077 | cytochrome P450, family 1, subfamily a, polypeptide 2 | 0.73 | 12.30 | 3.69 | 1.2e-03 | 1.1e-01 | -0.82 |
| 3060 | 1460474_at | 2610028L16Rik | 76368 | RIKEN cDNA 2610028L16 gene | 0.70 | 4.44 | 3.69 | 1.2e-03 | 1.1e-01 | -0.83 |
| 968 | 1426880_at | Etl4 | 208618 | enhancer trap locus 4 | -0.89 | 5.80 | -3.65 | 1.3e-03 | 1.2e-01 | -0.92 |
| 2981 | 1458245_at | Susd1 | 634731 | sushi domain containing 1 | -0.72 | 6.01 | -3.64 | 1.4e-03 | 1.2e-01 | -0.93 |
| 114 | 1416846_a_at | Pdzrn3 | 55983 | PDZ domain containing RING finger 3 | -1.09 | 5.41 | -3.60 | 1.5e-03 | 1.3e-01 | -1.02 |
| 2942 | 1457117_at | Nfe2l2 | 18024 | nuclear factor, erythroid derived 2, like 2 | -0.91 | 4.86 | -3.59 | 1.5e-03 | 1.3e-01 | -1.04 |
| 82 | 1416501_at | Pdpk1 | 18607 | 3-phosphoinositide dependent protein kinase 1 | 0.79 | 7.59 | 3.54 | 1.8e-03 | 1.3e-01 | -1.15 |
| 1507 | 1434861_at | Klhl28 | 66689 | kelch-like 28 | -0.68 | 6.14 | -3.55 | 1.7e-03 | 1.3e-01 | -1.13 |
| 1605 | 1435829_at | Zmat1 | 215693 | zinc finger, matrin type 1 | -0.89 | 6.09 | -3.54 | 1.7e-03 | 1.3e-01 | -1.14 |
| 771 | 1424591_at | Caap1 | 67770 | caspase activity and apoptosis inhibitor 1 | -0.64 | 6.25 | -3.50 | 1.9e-03 | 1.4e-01 | -1.23 |
| 788 | 1424687_at | Heatr6 | 217026 | HEAT repeat containing 6 | 0.85 | 4.37 | 3.45 | 2.2e-03 | 1.5e-01 | -1.34 |
| 1062 | 1427982_s_at | Syne2 | 319565 | spectrin repeat containing, nuclear envelope 2 | -0.76 | 5.87 | -3.45 | 2.2e-03 | 1.5e-01 | -1.34 |
| 1281 | 1430820_a_at | Bbx | 70508 | bobby sox HMG box containing | 0.90 | 5.18 | 3.47 | 2.1e-03 | 1.5e-01 | -1.30 |
| 1429 | 1434188_at | Slc16a12 | 240638 | solute carrier family 16 (monocarboxylic acid transporters), member 12 | -0.61 | 7.51 | -3.47 | 2.0e-03 | 1.5e-01 | -1.29 |
| 2611 | 1452438_s_at | Taf4 | 228980 | TATA-box binding protein associated factor 4 | -0.76 | 5.75 | -3.45 | 2.2e-03 | 1.5e-01 | -1.35 |
| 552 | 1421704_a_at | Pik3c2g | 18705 | phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma | -0.88 | 4.51 | -3.42 | 2.3e-03 | 1.5e-01 | -1.40 |
| 1926 | 1439397_at | Fmn1 | 14260 | formin 1 | -0.87 | 5.35 | -3.43 | 2.3e-03 | 1.5e-01 | -1.39 |
| 2116 | 1443825_x_at | Spaca3 | 75622 | sperm acrosome associated 3 | 0.53 | 4.16 | 3.42 | 2.4e-03 | 1.5e-01 | -1.41 |
| 1003 | 1427185_at | Mef2a | 17258 | myocyte enhancer factor 2A | -0.59 | 7.73 | -3.40 | 2.5e-03 | 1.5e-01 | -1.45 |
| 2812 | 1455434_a_at | Ktn1 | 16709 | kinectin 1 | -0.78 | 6.26 | -3.40 | 2.4e-03 | 1.5e-01 | -1.44 |
| 149 | 1417084_at | Eif4ebp2 | 13688 | eukaryotic translation initiation factor 4E binding protein 2 | 1.11 | 7.18 | 3.39 | 2.5e-03 | 1.5e-01 | -1.48 |
| 963 | 1426831_at | Ahcyl1 | 229709 | S-adenosylhomocysteine hydrolase-like 1 | -0.55 | 7.95 | -3.38 | 2.6e-03 | 1.5e-01 | -1.50 |
| 1152 | 1428846_at | Ttc14 | 67120 | tetratricopeptide repeat domain 14 | -0.73 | 3.95 | -3.36 | 2.7e-03 | 1.5e-01 | -1.53 |
| 1607 | 1435866_s_at | H2aw | 319162 | H2A.W histone | -0.65 | 5.80 | -3.36 | 2.7e-03 | 1.5e-01 | -1.53 |
| 1741 | 1437158_at | Nipbl | 71175 | NIPBL cohesin loading factor | 1.04 | 7.30 | 3.35 | 2.7e-03 | 1.5e-01 | -1.54 |
| 2538 | 1451791_at | Tfpi | 21788 | tissue factor pathway inhibitor | -0.73 | 5.07 | -3.34 | 2.9e-03 | 1.5e-01 | -1.58 |
| 1204 | 1429327_at | Nemf | 66244 | nuclear export mediator factor | 0.86 | 5.77 | 3.31 | 3.1e-03 | 1.6e-01 | -1.64 |
| 1612 | 1435904_at | Ago3 | 214150 | argonaute RISC catalytic subunit 3 | -0.62 | 4.40 | -3.30 | 3.1e-03 | 1.6e-01 | -1.65 |
| 221 | 1417791_a_at | Zfp638 | 18139 | zinc finger protein 638 | -0.57 | 7.13 | -3.29 | 3.2e-03 | 1.6e-01 | -1.67 |
| 1494 | 1434770_at | Iqcb1 | 320299 | IQ calmodulin-binding motif containing 1 | -0.62 | 4.56 | -3.27 | 3.4e-03 | 1.7e-01 | -1.72 |
| 2920 | 1456625_at | Aasdhppt | 67618 | aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase | -0.63 | 5.45 | -3.26 | 3.5e-03 | 1.7e-01 | -1.75 |
| 882 | 1425673_at | Lpp | 210126 | LIM domain containing preferred translocation partner in lipoma | 0.59 | 6.43 | 3.23 | 3.7e-03 | 1.8e-01 | -1.81 |
| 1649 | 1436404_at | Tlcd1 | 68385 | TLC domain containing 1 | -0.57 | 6.66 | -3.23 | 3.7e-03 | 1.8e-01 | -1.80 |
| 2887 | 1456156_at | Lepr | 16847 | leptin receptor | -1.78 | 5.12 | -3.22 | 3.7e-03 | 1.8e-01 | -1.82 |
| 12 | 1415859_at | Eif3c | 56347 | eukaryotic translation initiation factor 3, subunit C | 0.82 | 8.92 | 3.22 | 3.8e-03 | 1.8e-01 | -1.83 |
| 671 | 1423342_at | Barx1 | 12022 | BarH-like homeobox 1 | 0.58 | 4.79 | 3.20 | 3.9e-03 | 1.8e-01 | -1.86 |
| 453 | 1419915_at | Nus1 | 52014 | NUS1 dehydrodolichyl diphosphate synthase subunit | -0.60 | 4.80 | -3.18 | 4.2e-03 | 1.8e-01 | -1.91 |
| 494 | 1420715_a_at | Pparg | 19016 | peroxisome proliferator activated receptor gamma | -0.75 | 5.98 | -3.17 | 4.2e-03 | 1.8e-01 | -1.92 |
| 798 | 1424770_at | Cald1 | 109624 | caldesmon 1 | 0.72 | 10.22 | 3.18 | 4.2e-03 | 1.8e-01 | -1.92 |
| 1659 | 1436499_at | Sgms1 | 208449 | sphingomyelin synthase 1 | -0.82 | 7.15 | -3.17 | 4.2e-03 | 1.8e-01 | -1.93 |
| 2150 | 1444437_at | Usp34 | 17847 | ubiquitin specific peptidase 34 | -0.80 | 3.95 | -3.17 | 4.2e-03 | 1.8e-01 | -1.92 |
| 1674 | 1436594_at | Zfp719 | 210105 | zinc finger protein 719 | -0.68 | 4.60 | -3.17 | 4.3e-03 | 1.8e-01 | -1.94 |
| 185 | 1417409_at | Jun | 16476 | jun proto-oncogene | -1.32 | 6.97 | -3.13 | 4.7e-03 | 1.8e-01 | -2.01 |
| 263 | 1418098_at | Adcy4 | 104110 | adenylate cyclase 4 | -0.53 | 4.94 | -3.13 | 4.7e-03 | 1.8e-01 | -2.01 |
Tabla 12: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta DHA.
Control vs Diet-Restriction (CT vs DR):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 479 | 1420531_at | Hsd3b5 | 15496 | hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 5 | -8.33 | 11.21 | -27.74 | 3.1e-19 | 9.5e-16 | 33.47 |
| 495 | 1420722_at | Elovl3 | 12686 | elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3 | -7.00 | 11.47 | -23.62 | 1.1e-17 | 1.7e-14 | 30.23 |
| 879 | 1425645_s_at | Cyp2b10 | 13088 | cytochrome P450, family 2, subfamily b, polypeptide 10 | 6.52 | 4.58 | 22.52 | 3.2e-17 | 3.3e-14 | 29.25 |
| 444 | 1419759_at | Abcb1a | 18671 | ATP-binding cassette, sub-family B (MDR/TAP), member 1A | 3.35 | 4.77 | 19.33 | 9.2e-16 | 7.1e-13 | 26.07 |
| 634 | 1422925_s_at | Acot3 | 171281 | acyl-CoA thioesterase 3 | 5.09 | 6.17 | 18.96 | 1.4e-15 | 8.6e-13 | 25.67 |
| 2386 | 1449844_at | Slco1a1 | 28248 | solute carrier organic anion transporter family, member 1a1 | -4.74 | 8.95 | -17.99 | 4.4e-15 | 2.3e-12 | 24.57 |
| 426 | 1419590_at | Cyp2b9 | 13094 | cytochrome P450, family 2, subfamily b, polypeptide 9 | 7.38 | 4.64 | 14.86 | 2.6e-13 | 1.1e-10 | 20.59 |
| 2364 | 1449479_at | Cyp2b13 | 13089 | cytochrome P450, family 2, subfamily b, polypeptide 13 | 3.36 | 4.39 | 14.70 | 3.3e-13 | 1.3e-10 | 20.37 |
| 126 | 1416933_at | Por | 18984 | P450 (cytochrome) oxidoreductase | 3.59 | 8.69 | 14.54 | 4.1e-13 | 1.4e-10 | 20.14 |
| 1965 | 1439934_at | Slc30a10 | 226781 | solute carrier family 30, member 10 | -2.42 | 7.85 | -14.35 | 5.3e-13 | 1.6e-10 | 19.88 |
| 2770 | 1455025_at | Paqr9 | 75552 | progestin and adipoQ receptor family member IX | -2.76 | 10.41 | -13.91 | 1.0e-12 | 2.9e-10 | 19.23 |
| 846 | 1425303_at | Gck | 103988 | glucokinase | -3.20 | 8.61 | -13.71 | 1.4e-12 | 3.5e-10 | 18.94 |
| 343 | 1418780_at | Cyp39a1 | 56050 | cytochrome P450, family 39, subfamily a, polypeptide 1 | 3.01 | 7.66 | 13.52 | 1.9e-12 | 4.1e-10 | 18.64 |
| 2879 | 1456074_at | Sdr9c7 | 70061 | 4short chain dehydrogenase/reductase family 9C, member 7 | -2.35 | 7.22 | -13.52 | 1.8e-12 | 4.1e-10 | 18.66 |
| 2983 | 1458284_at | Ptbp1 | 19205 | polypyrimidine tract binding protein 1 | -2.85 | 7.67 | -13.03 | 4.0e-12 | 8.1e-10 | 17.89 |
| 1060 | 1427963_s_at | Rdh9 | 103142 | retinol dehydrogenase 9 | 2.37 | 9.52 | 12.65 | 7.2e-12 | 1.4e-09 | 17.30 |
| 711 | 1423891_at | Gstt3 | 103140 | glutathione S-transferase, theta 3 | 2.60 | 8.69 | 12.46 | 9.7e-12 | 1.8e-09 | 16.99 |
| 776 | 1424629_at | Brca1 | 12189 | breast cancer 1, early onset | 2.23 | 3.74 | 12.34 | 1.2e-11 | 1.8e-09 | 16.80 |
| 1021 | 1427347_s_at | Tubb2a | 22151 | tubulin, beta 2A class IIA | -3.04 | 11.00 | -12.35 | 1.2e-11 | 1.8e-09 | 16.81 |
| 3037 | 1460196_at | Cbr1 | 12408 | carbonyl reductase 1 | 1.84 | 9.57 | 12.34 | 1.2e-11 | 1.8e-09 | 16.79 |
| 242 | 1417883_at | Gstt2 | 14872 | glutathione S-transferase, theta 2 | 2.56 | 8.94 | 12.29 | 1.3e-11 | 1.9e-09 | 16.71 |
| 2544 | 1451814_a_at | Htatip2 | 53415 | HIV-1 Tat interactive protein 2 | 1.63 | 8.80 | 12.26 | 1.4e-11 | 1.9e-09 | 16.67 |
| 2371 | 1449565_at | Cyp2g1 | 13108 | cytochrome P450, family 2, subfamily g, polypeptide 1 | 2.44 | 4.83 | 11.99 | 2.1e-11 | 2.8e-09 | 16.21 |
| 852 | 1425343_at | Hdhd3 | 72748 | haloacid dehalogenase-like hydrolase domain containing 3 | -2.05 | 7.03 | -11.93 | 2.4e-11 | 3.0e-09 | 16.11 |
| 1034 | 1427474_s_at | Gstm3 | 14864 | glutathione S-transferase, mu 3 | 3.35 | 9.62 | 11.87 | 2.6e-11 | 3.2e-09 | 16.01 |
| 1463 | 1434465_x_at | Vldlr | 22359 | very low density lipoprotein receptor | 3.11 | 4.75 | 11.76 | 3.1e-11 | 3.7e-09 | 15.83 |
| 984 | 1427042_at | Mal2 | 105853 | mal, T cell differentiation protein 2 | -2.08 | 7.73 | -11.73 | 3.3e-11 | 3.7e-09 | 15.78 |
| 2344 | 1449308_at | C6 | 12274 | complement component 6 | -2.77 | 9.91 | -11.71 | 3.4e-11 | 3.7e-09 | 15.75 |
| 525 | 1421092_at | Serpina12 | 68054 | serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12 | -4.42 | 10.58 | -11.26 | 7.4e-11 | 7.9e-09 | 14.96 |
| 2674 | 1453259_at | Insc | 233752 | INSC spindle orientation adaptor protein | -2.08 | 8.06 | -11.05 | 1.1e-10 | 1.1e-08 | 14.59 |
| 1065 | 1428012_at | C8a | 230558 | complement component 8, alpha polypeptide | -1.88 | 12.38 | -10.74 | 1.9e-10 | 1.8e-08 | 14.03 |
| 1318 | 1431806_at | 4931408D14Rik | 77059 | RIKEN cDNA 4931408D14 gene | 2.43 | 6.63 | 10.73 | 1.9e-10 | 1.8e-08 | 14.03 |
| 10 | 1415840_at | Elovl5 | 68801 | ELOVL family member 5, elongation of long chain fatty acids (yeast) | -2.06 | 12.87 | -10.54 | 2.7e-10 | 2.5e-08 | 13.68 |
| 67 | 1416368_at | Gsta4 | 14860 | glutathione S-transferase, alpha 4 | 2.43 | 9.39 | 10.53 | 2.7e-10 | 2.5e-08 | 13.65 |
| 311 | 1418488_s_at | Ripk4 | 72388 | receptor-interacting serine-threonine kinase 4 | 1.80 | 6.26 | 10.41 | 3.4e-10 | 3.0e-08 | 13.44 |
| 821 | 1424973_at | Cyp3a25 | 56388 | cytochrome P450, family 3, subfamily a, polypeptide 25 | 1.69 | 12.22 | 10.38 | 3.6e-10 | 3.1e-08 | 13.38 |
| 690 | 1423627_at | Nqo1 | 18104 | NAD(P)H dehydrogenase, quinone 1 | 2.50 | 5.75 | 10.25 | 4.6e-10 | 3.6e-08 | 13.14 |
| 1163 | 1428923_at | Ppp1r3g | 76487 | protein phosphatase 1, regulatory subunit 3G | 5.34 | 4.81 | 10.25 | 4.6e-10 | 3.6e-08 | 13.14 |
| 1643 | 1436293_x_at | Ildr2 | 100039795 | immunoglobulin-like domain containing receptor 2 | 2.77 | 7.86 | 10.27 | 4.4e-10 | 3.6e-08 | 13.17 |
| 750 | 1424352_at | Cyp4a12a | 277753 | cytochrome P450, family 4, subfamily a, polypeptide 12a | -4.03 | 10.66 | -10.20 | 5.0e-10 | 3.8e-08 | 13.05 |
| 2815 | 1455454_at | Akr1c19 | 432720 | aldo-keto reductase family 1, member C19 | 1.91 | 9.30 | 10.17 | 5.3e-10 | 4.0e-08 | 12.98 |
| 2127 | 1443908_at | Gm19696 | 100503447 | predicted gene, 19696 | -1.53 | 7.17 | -10.12 | 5.8e-10 | 4.3e-08 | 12.90 |
| 470 | 1420405_at | Slco1a4 | 28250 | solute carrier organic anion transporter family, member 1a4 | 3.47 | 8.17 | 10.10 | 6.1e-10 | 4.3e-08 | 12.85 |
| 1431 | 1434202_a_at | Fam107a | 268709 | family with sequence similarity 107, member A | 3.16 | 3.45 | 10.09 | 6.1e-10 | 4.3e-08 | 12.84 |
| 2698 | 1453685_at | Nudt7 | 67528 | nudix (nucleoside diphosphate linked moiety X)-type motif 7 | -1.64 | 6.68 | -10.07 | 6.4e-10 | 4.4e-08 | 12.79 |
| 2420 | 1450484_a_at | Cmpk2 | 22169 | cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial | -2.20 | 6.36 | -9.79 | 1.1e-09 | 7.3e-08 | 12.26 |
| 578 | 1422076_at | Acot4 | 171282 | acyl-CoA thioesterase 4 | 1.89 | 5.13 | 9.76 | 1.2e-09 | 7.4e-08 | 12.20 |
| 848 | 1425314_at | Adgrv1 | 110789 | adhesion G protein-coupled receptor V1 | -2.42 | 6.31 | -9.76 | 1.1e-09 | 7.4e-08 | 12.21 |
| 2317 | 1448978_at | Ngef | 53972 | neuronal guanine nucleotide exchange factor | 1.64 | 6.94 | 9.72 | 1.2e-09 | 7.8e-08 | 12.14 |
| 360 | 1418936_at | Maff | 17133 | v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian) | 1.94 | 5.51 | 9.63 | 1.5e-09 | 9.1e-08 | 11.96 |
| 880 | 1425646_at | Nmrk1 | 225994 | nicotinamide riboside kinase 1 | 1.77 | 6.17 | 9.42 | 2.2e-09 | 1.3e-07 | 11.54 |
| 2446 | 1450830_a_at | Pde6c | 110855 | phosphodiesterase 6C, cGMP specific, cone, alpha prime | 2.37 | 3.69 | 9.42 | 2.3e-09 | 1.3e-07 | 11.53 |
| 156 | 1417168_a_at | Usp2 | 53376 | ubiquitin specific peptidase 2 | 4.80 | 6.63 | 9.40 | 2.3e-09 | 1.3e-07 | 11.50 |
| 721 | 1424033_at | Srsf7 | 225027 | serine/arginine-rich splicing factor 7 | -2.02 | 6.91 | -9.37 | 2.5e-09 | 1.4e-07 | 11.44 |
| 2223 | 1447854_s_at | H2bc21 | 319190 | H2B clustered histone 21 | -2.00 | 5.22 | -9.35 | 2.6e-09 | 1.4e-07 | 11.40 |
| 1104 | 1428487_s_at | Coq10b | 67876 | coenzyme Q10B | 2.18 | 7.38 | 9.27 | 3.0e-09 | 1.7e-07 | 11.24 |
| 1294 | 1431101_a_at | Srd5a1 | 78925 | steroid 5 alpha-reductase 1 | -1.69 | 7.92 | -9.26 | 3.1e-09 | 1.7e-07 | 11.22 |
| 2461 | 1450966_at | Crot | 74114 | carnitine O-octanoyltransferase | -1.64 | 11.88 | -9.24 | 3.2e-09 | 1.7e-07 | 11.18 |
| 251 | 1417981_at | Insig2 | 72999 | insulin induced gene 2 | -1.89 | 11.61 | -9.23 | 3.3e-09 | 1.7e-07 | 11.16 |
| 1014 | 1427258_at | Trim24 | 21848 | tripartite motif-containing 24 | 2.45 | 6.15 | 9.21 | 3.4e-09 | 1.7e-07 | 11.12 |
| 1012 | 1427249_x_at | Mup3 | 17842 | major urinary protein 3 | -2.38 | 4.58 | -9.20 | 3.5e-09 | 1.7e-07 | 11.10 |
| 1238 | 1429899_at | 5730414N17Rik | 70524 | RIKEN cDNA 5730414N17 gene | -1.83 | 7.32 | -9.13 | 4.0e-09 | 2.0e-07 | 10.95 |
| 2274 | 1448502_at | Slc16a7 | 20503 | solute carrier family 16 (monocarboxylic acid transporters), member 7 | 1.79 | 9.15 | 9.11 | 4.2e-09 | 2.0e-07 | 10.91 |
| 2399 | 1450048_a_at | Idh2 | 269951 | isocitrate dehydrogenase 2 (NADP+), mitochondrial | 1.38 | 8.64 | 9.06 | 4.6e-09 | 2.2e-07 | 10.82 |
| 1466 | 1434473_at | Slc16a5 | 217316 | solute carrier family 16 (monocarboxylic acid transporters), member 5 | 3.77 | 5.44 | 9.04 | 4.8e-09 | 2.3e-07 | 10.77 |
| 520 | 1421040_a_at | Gsta2 | 14858 | glutathione S-transferase, alpha 2 (Yc2) | 3.49 | 10.11 | 8.98 | 5.4e-09 | 2.5e-07 | 10.65 |
| 2804 | 1455293_at | Leo1 | 235497 | Leo1, Paf1/RNA polymerase II complex component | -1.54 | 7.04 | -8.86 | 6.8e-09 | 3.1e-07 | 10.41 |
| 485 | 1420630_at | Fam234b | 74525 | family with sequence similarity 234, member B | 1.30 | 7.05 | 8.85 | 7.0e-09 | 3.2e-07 | 10.39 |
| 661 | 1423257_at | Cyp4a14 | 13119 | cytochrome P450, family 4, subfamily a, polypeptide 14 | 6.95 | 8.78 | 8.81 | 7.7e-09 | 3.4e-07 | 10.30 |
| 270 | 1418133_at | Bcl3 | 12051 | B cell leukemia/lymphoma 3 | -1.99 | 6.87 | -8.79 | 7.9e-09 | 3.5e-07 | 10.26 |
| 1033 | 1427472_a_at | C8b | 110382 | complement component 8, beta polypeptide | -1.76 | 10.31 | -8.73 | 9.0e-09 | 3.9e-07 | 10.13 |
| 2551 | 1451903_at | Kynu | 70789 | kynureninase | -1.44 | 5.68 | -8.70 | 9.6e-09 | 4.1e-07 | 10.07 |
| 1629 | 1436181_at | Asap2 | 211914 | ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 | -2.26 | 6.74 | -8.68 | 9.8e-09 | 4.1e-07 | 10.05 |
| 1285 | 1430893_at | Mup10 | 100039008 | major urinary protein 10 | -2.75 | 9.35 | -8.65 | 1.1e-08 | 4.3e-07 | 9.97 |
| 2248 | 1448300_at | Mgst3 | 66447 | microsomal glutathione S-transferase 3 | 1.62 | 7.99 | 8.65 | 1.1e-08 | 4.3e-07 | 9.97 |
Tabla 13: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta DR.
Control vs EFA-Deficient Diet (CTvsEFA):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 215 | 1417761_at | Apoa4 | 11808 | apolipoprotein A-IV | 2.43 | 10.92 | 7.45 | 1.4e-07 | 2.2e-04 | 7.46 |
| 1956 | 1439804_at | 2310015A10Rik | 69548 | RIKEN cDNA 2310015A10 gene | 1.34 | 4.58 | 7.44 | 1.4e-07 | 2.2e-04 | 7.45 |
| 848 | 1425314_at | Adgrv1 | 110789 | adhesion G protein-coupled receptor V1 | -1.76 | 6.31 | -7.13 | 2.8e-07 | 2.9e-04 | 6.82 |
| 2133 | 1444021_at | Sqstm1 | 18412 | sequestosome 1 | 1.22 | 4.67 | 6.54 | 1.1e-06 | 8.2e-04 | 5.57 |
| 2904 | 1456377_x_at | Limd2 | 67803 | LIM domain containing 2 | -1.13 | 8.65 | -6.46 | 1.3e-06 | 8.2e-04 | 5.41 |
| 1342 | 1432650_at | 2510019K15Rik | 67142 | RIKEN cDNA 2510019K15 gene | 1.54 | 7.16 | 5.88 | 5.3e-06 | 2.7e-03 | 4.12 |
| 2730 | 1454685_at | Gpr146 | 80290 | G protein-coupled receptor 146 | -1.19 | 8.09 | -5.72 | 7.9e-06 | 3.5e-03 | 3.76 |
| 2977 | 1458049_at | Hgd | 15233 | homogentisate 1, 2-dioxygenase | 1.25 | 6.20 | 5.61 | 1.0e-05 | 3.9e-03 | 3.52 |
| 2903 | 1456354_at | Chrna4 | 11438 | cholinergic receptor, nicotinic, alpha polypeptide 4 | 1.55 | 4.23 | 5.50 | 1.3e-05 | 4.6e-03 | 3.27 |
| 449 | 1419874_x_at | Zbtb16 | 235320 | zinc finger and BTB domain containing 16 | -2.24 | 6.64 | -5.28 | 2.3e-05 | 6.5e-03 | 2.76 |
| 2879 | 1456074_at | Sdr9c7 | 70061 | 4short chain dehydrogenase/reductase family 9C, member 7 | -0.92 | 7.22 | -5.30 | 2.2e-05 | 6.5e-03 | 2.81 |
| 239 | 1417877_at | Eepd1 | 67484 | endonuclease/exonuclease/phosphatase family domain containing 1 | 0.84 | 6.55 | 5.19 | 2.9e-05 | 7.4e-03 | 2.56 |
| 286 | 1418265_s_at | Irf2 | 16363 | interferon regulatory factor 2 | -0.86 | 8.11 | -5.09 | 3.7e-05 | 8.4e-03 | 2.34 |
| 1198 | 1429262_at | Rassf6 | 73246 | Ras association (RalGDS/AF-6) domain family member 6 | 1.01 | 6.54 | 5.02 | 4.4e-05 | 8.4e-03 | 2.16 |
| 1383 | 1433768_at | Palld | 72333 | palladin, cytoskeletal associated protein | 0.89 | 8.72 | 5.00 | 4.7e-05 | 8.4e-03 | 2.11 |
| 1886 | 1438842_at | Mtch2 | 56428 | mitochondrial carrier 2 | 1.20 | 3.78 | 5.05 | 4.1e-05 | 8.4e-03 | 2.23 |
| 2171 | 1445669_at | Spry4 | 24066 | sprouty RTK signaling antagonist 4 | -1.39 | 5.94 | -5.05 | 4.1e-05 | 8.4e-03 | 2.23 |
| 1209 | 1429396_at | Atg16l2 | 73683 | autophagy related 16-like 2 (S. cerevisiae) | 1.33 | 6.11 | 4.96 | 5.1e-05 | 8.7e-03 | 2.03 |
| 1996 | 1440444_at | Fads1 | 76267 | fatty acid desaturase 1 | 1.27 | 5.89 | 4.85 | 6.7e-05 | 1.1e-02 | 1.77 |
| 763 | 1424504_at | Rab22a | 19334 | RAB22A, member RAS oncogene family | 0.90 | 5.69 | 4.73 | 9.0e-05 | 1.4e-02 | 1.50 |
| 457 | 1419985_s_at | Ccdc69 | 52570 | coiled-coil domain containing 69 | 0.83 | 2.79 | 4.68 | 1.0e-04 | 1.4e-02 | 1.37 |
| 1781 | 1437633_at | Ankrd11 | 77087 | ankyrin repeat domain 11 | 0.82 | 6.60 | 4.69 | 9.9e-05 | 1.4e-02 | 1.41 |
| 1177 | 1429049_at | Nuak2 | 74137 | NUAK family, SNF1-like kinase, 2 | -0.83 | 7.08 | -4.65 | 1.1e-04 | 1.5e-02 | 1.31 |
| 2186 | 1446316_at | Lpin2 | 64898 | lipin 2 | 1.95 | 5.14 | 4.61 | 1.2e-04 | 1.6e-02 | 1.22 |
| 1926 | 1439397_at | Fmn1 | 14260 | formin 1 | 1.16 | 5.35 | 4.58 | 1.3e-04 | 1.6e-02 | 1.15 |
| 357 | 1418918_at | Igfbp1 | 16006 | insulin-like growth factor binding protein 1 | 2.71 | 10.86 | 4.51 | 1.6e-04 | 1.6e-02 | 0.98 |
| 1534 | 1435158_at | Rbm12b1 | 72397 | RNA binding motif protein 12 B1 | 1.25 | 4.61 | 4.44 | 1.9e-04 | 1.6e-02 | 0.82 |
| 1840 | 1438242_at | Usp40 | 227334 | ubiquitin specific peptidase 40 | 0.79 | 5.88 | 4.48 | 1.7e-04 | 1.6e-02 | 0.92 |
| 1855 | 1438450_at | Lin7a | 108030 | lin-7 homolog A (C. elegans) | -0.76 | 6.69 | -4.43 | 1.9e-04 | 1.6e-02 | 0.81 |
| 1871 | 1438643_at | Camk1d | 227541 | calcium/calmodulin-dependent protein kinase ID | 1.41 | 7.00 | 4.54 | 1.5e-04 | 1.6e-02 | 1.05 |
| 1954 | 1439795_at | Adgrg2 | 237175 | adhesion G protein-coupled receptor G2 | -0.77 | 3.24 | -4.50 | 1.6e-04 | 1.6e-02 | 0.97 |
| 2002 | 1440576_at | Cpn1 | 93721 | carboxypeptidase N, polypeptide 1 | 1.07 | 6.82 | 4.50 | 1.6e-04 | 1.6e-02 | 0.95 |
| 2397 | 1450035_a_at | Prpf40a | 56194 | pre-mRNA processing factor 40A | 1.12 | 6.91 | 4.45 | 1.8e-04 | 1.6e-02 | 0.85 |
| 2900 | 1456327_at | A530020G20Rik | 319839 | RIKEN cDNA A530020G20 gene | 1.11 | 4.44 | 4.55 | 1.4e-04 | 1.6e-02 | 1.09 |
| 3020 | 1459909_at | Nfix | 18032 | nuclear factor I/X | -0.99 | 6.32 | -4.45 | 1.8e-04 | 1.6e-02 | 0.85 |
| 3076 | 1460729_at | Rock1 | 19877 | Rho-associated coiled-coil containing protein kinase 1 | 1.00 | 6.35 | 4.45 | 1.8e-04 | 1.6e-02 | 0.84 |
| 1830 | 1438169_a_at | Frmd4b | 232288 | FERM domain containing 4B | 0.96 | 10.28 | 4.41 | 2.0e-04 | 1.7e-02 | 0.76 |
| 2219 | 1447791_s_at | Gna14 | 14675 | guanine nucleotide binding protein, alpha 14 | -0.82 | 3.87 | -4.38 | 2.2e-04 | 1.7e-02 | 0.68 |
| 1354 | 1433481_at | Fkbp14 | 231997 | FK506 binding protein 14 | 0.93 | 5.80 | 4.37 | 2.2e-04 | 1.8e-02 | 0.65 |
| 1238 | 1429899_at | 5730414N17Rik | 70524 | RIKEN cDNA 5730414N17 gene | -0.87 | 7.32 | -4.33 | 2.5e-04 | 1.8e-02 | 0.56 |
| 2103 | 1443327_at | D130043K22Rik | 210108 | RIKEN cDNA D130043K22 gene | 1.17 | 5.40 | 4.34 | 2.4e-04 | 1.8e-02 | 0.60 |
| 2539 | 1451799_at | Ccdc25 | 67179 | coiled-coil domain containing 25 | 1.33 | 4.79 | 4.33 | 2.4e-04 | 1.8e-02 | 0.57 |
| 259 | 1418069_at | Apoc2 | 11813 | apolipoprotein C-II | 0.77 | 12.31 | 4.32 | 2.5e-04 | 1.8e-02 | 0.54 |
| 167 | 1417273_at | Pdk4 | 27273 | pyruvate dehydrogenase kinase, isoenzyme 4 | 2.31 | 6.66 | 4.28 | 2.8e-04 | 1.9e-02 | 0.46 |
| 963 | 1426831_at | Ahcyl1 | 229709 | S-adenosylhomocysteine hydrolase-like 1 | 0.69 | 7.95 | 4.27 | 2.9e-04 | 2.0e-02 | 0.42 |
| 339 | 1418760_at | Rdh11 | 17252 | retinol dehydrogenase 11 | 1.26 | 8.71 | 4.24 | 3.1e-04 | 2.0e-02 | 0.36 |
| 931 | 1426485_at | Ubxn4 | 67812 | UBX domain protein 4 | 1.18 | 9.64 | 4.24 | 3.1e-04 | 2.0e-02 | 0.36 |
| 2393 | 1449945_at | Ppargc1b | 170826 | peroxisome proliferative activated receptor, gamma, coactivator 1 beta | -0.91 | 7.79 | -4.25 | 3.0e-04 | 2.0e-02 | 0.37 |
| 1153 | 1428851_at | Pxdc1 | 66895 | PX domain containing 1 | 0.85 | 9.92 | 4.22 | 3.2e-04 | 2.0e-02 | 0.31 |
| 361 | 1418940_at | Sult1b1 | 56362 | sulfotransferase family 1B, member 1 | -0.68 | 7.93 | -4.18 | 3.6e-04 | 2.1e-02 | 0.22 |
| 485 | 1420630_at | Fam234b | 74525 | family with sequence similarity 234, member B | -0.61 | 7.05 | -4.19 | 3.5e-04 | 2.1e-02 | 0.24 |
| 2722 | 1454558_at | 5430416B10Rik | 71430 | RIKEN cDNA 5430416B10 gene | 1.16 | 4.98 | 4.18 | 3.6e-04 | 2.1e-02 | 0.22 |
| 2179 | 1445881_at | 2310035P21Rik | 75683 | RIKEN cDNA 2310035P21 gene | 1.64 | 4.62 | 4.16 | 3.8e-04 | 2.1e-02 | 0.16 |
| 2467 | 1451022_at | Lrp6 | 16974 | low density lipoprotein receptor-related protein 6 | 0.74 | 5.74 | 4.17 | 3.7e-04 | 2.1e-02 | 0.19 |
| 2640 | 1452864_at | Med12l | 329650 | mediator complex subunit 12-like | -0.67 | 4.80 | -4.16 | 3.8e-04 | 2.1e-02 | 0.17 |
| 278 | 1418209_a_at | Pfn2 | 18645 | profilin 2 | -0.93 | 6.13 | -4.12 | 4.1e-04 | 2.3e-02 | 0.08 |
| 798 | 1424770_at | Cald1 | 109624 | caldesmon 1 | 0.93 | 10.22 | 4.12 | 4.2e-04 | 2.3e-02 | 0.07 |
| 2932 | 1456914_at | Slc16a4 | 229699 | solute carrier family 16 (monocarboxylic acid transporters), member 4 | 1.20 | 4.44 | 4.06 | 4.9e-04 | 2.6e-02 | -0.07 |
| 1294 | 1431101_a_at | Srd5a1 | 78925 | steroid 5 alpha-reductase 1 | 0.74 | 7.92 | 4.03 | 5.1e-04 | 2.6e-02 | -0.12 |
| 1849 | 1438404_at | Rnf144a | 108089 | ring finger protein 144A | 0.80 | 6.60 | 4.04 | 5.1e-04 | 2.6e-02 | -0.11 |
| 2095 | 1443046_at | Abcd3 | 19299 | ATP-binding cassette, sub-family D (ALD), member 3 | 1.00 | 4.16 | 4.02 | 5.3e-04 | 2.7e-02 | -0.14 |
| 1148 | 1428832_at | Tedc2 | 72016 | tubulin epsilon and delta complex 2 | -0.93 | 8.97 | -4.01 | 5.4e-04 | 2.7e-02 | -0.17 |
| 788 | 1424687_at | Heatr6 | 217026 | HEAT repeat containing 6 | 0.98 | 4.37 | 4.01 | 5.5e-04 | 2.7e-02 | -0.19 |
| 1339 | 1432543_a_at | Klf13 | 50794 | Kruppel-like factor 13 | -0.82 | 7.48 | -4.00 | 5.6e-04 | 2.7e-02 | -0.21 |
| 1460 | 1434449_at | Aqp4 | 11829 | aquaporin 4 | 1.32 | 4.93 | 3.99 | 5.7e-04 | 2.7e-02 | -0.21 |
| 2069 | 1442277_at | Chka | 12660 | choline kinase alpha | 1.72 | 7.10 | 3.99 | 5.8e-04 | 2.7e-02 | -0.23 |
| 94 | 1416661_at | Eif3a | 13669 | eukaryotic translation initiation factor 3, subunit A | 0.99 | 7.41 | 3.97 | 6.0e-04 | 2.7e-02 | -0.27 |
| 415 | 1419499_at | Gpam | 14732 | glycerol-3-phosphate acyltransferase, mitochondrial | 0.99 | 12.03 | 3.97 | 6.0e-04 | 2.7e-02 | -0.26 |
| 720 | 1424029_at | Tspyl4 | 72480 | TSPY-like 4 | 1.31 | 6.04 | 3.93 | 6.7e-04 | 2.9e-02 | -0.37 |
| 1021 | 1427347_s_at | Tubb2a | 22151 | tubulin, beta 2A class IIA | 0.97 | 11.00 | 3.93 | 6.6e-04 | 2.9e-02 | -0.36 |
| 569 | 1421957_a_at | Pcyt1a | 13026 | phosphate cytidylyltransferase 1, choline, alpha isoform | 0.63 | 7.22 | 3.90 | 7.2e-04 | 3.1e-02 | -0.43 |
| 356 | 1418858_at | Aox3 | 71724 | aldehyde oxidase 3 | -1.10 | 11.36 | -3.87 | 7.8e-04 | 3.2e-02 | -0.51 |
| 1740 | 1437129_at | Oga | 76055 | O-GlcNAcase | 1.14 | 5.01 | 3.87 | 7.8e-04 | 3.2e-02 | -0.51 |
| 1879 | 1438752_at | A230058F20Rik | 320270 | RIKEN cDNA A230058F20 gene | 0.85 | 3.03 | 3.88 | 7.6e-04 | 3.2e-02 | -0.49 |
| 2552 | 1451920_a_at | Rfc1 | 19687 | replication factor C (activator 1) 1 | 1.02 | 5.11 | 3.88 | 7.6e-04 | 3.2e-02 | -0.48 |
Tabla 14: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta EFA.
Control vs High fat Diet (CTvsHF):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 236 | 1417867_at | Cfd | 11537 | complement factor D (adipsin) | 3.09 | 4.94 | 8.43 | 1.7e-08 | 5.1e-05 | 9.54 |
| 2810 | 1455387_at | Nufip2 | 68564 | nuclear fragile X mental retardation protein interacting protein 2 | -1.52 | 7.17 | -7.93 | 4.8e-08 | 7.4e-05 | 8.56 |
| 2431 | 1450715_at | Cyp1a2 | 13077 | cytochrome P450, family 1, subfamily a, polypeptide 2 | 1.45 | 12.30 | 7.38 | 1.6e-07 | 1.6e-04 | 7.44 |
| 3 | 1415776_at | Aldh3a2 | 11671 | aldehyde dehydrogenase family 3, subfamily A2 | 1.50 | 9.67 | 6.66 | 8.4e-07 | 4.2e-04 | 5.89 |
| 661 | 1423257_at | Cyp4a14 | 13119 | cytochrome P450, family 4, subfamily a, polypeptide 14 | 5.26 | 8.78 | 6.66 | 8.3e-07 | 4.2e-04 | 5.90 |
| 763 | 1424504_at | Rab22a | 19334 | RAB22A, member RAS oncogene family | 1.26 | 5.69 | 6.60 | 9.6e-07 | 4.2e-04 | 5.77 |
| 2708 | 1454067_a_at | 4931406C07Rik | 70984 | RIKEN cDNA 4931406C07 gene | 1.24 | 9.72 | 6.65 | 8.5e-07 | 4.2e-04 | 5.88 |
| 239 | 1417877_at | Eepd1 | 67484 | endonuclease/exonuclease/phosphatase family domain containing 1 | 1.06 | 6.55 | 6.54 | 1.1e-06 | 4.2e-04 | 5.64 |
| 640 | 1423078_a_at | Msmo1 | 66234 | methylsterol monoxygenase 1 | 1.26 | 9.92 | 6.39 | 1.6e-06 | 5.3e-04 | 5.29 |
| 1528 | 1435097_at | Mmab | 77697 | methylmalonic aciduria (cobalamin deficiency) cblB type homolog (human) | 1.13 | 5.07 | 6.35 | 1.7e-06 | 5.3e-04 | 5.21 |
| 637 | 1422964_at | Rad23a | 19358 | RAD23 homolog A, nucleotide excision repair protein | 1.04 | 6.79 | 6.12 | 3.0e-06 | 8.4e-04 | 4.69 |
| 711 | 1423891_at | Gstt3 | 103140 | glutathione S-transferase, theta 3 | 1.26 | 8.69 | 6.06 | 3.4e-06 | 8.8e-04 | 4.56 |
| 237 | 1417871_at | Hsd17b7 | 15490 | hydroxysteroid (17-beta) dehydrogenase 7 | 1.36 | 7.23 | 5.99 | 4.0e-06 | 9.5e-04 | 4.41 |
| 26 | 1416022_at | Fabp5 | 16592 | fatty acid binding protein 5, epidermal | -2.96 | 8.60 | -5.88 | 5.4e-06 | 1.1e-03 | 4.14 |
| 2026 | 1441098_at | Pnldc1 | 240023 | poly(A)-specific ribonuclease (PARN)-like domain containing 1 | 1.34 | 5.14 | 5.87 | 5.5e-06 | 1.1e-03 | 4.12 |
| 1776 | 1437594_x_at | Pigt | 78928 | phosphatidylinositol glycan anchor biosynthesis, class T | -1.03 | 5.96 | -5.79 | 6.6e-06 | 1.3e-03 | 3.94 |
| 879 | 1425645_s_at | Cyp2b10 | 13088 | cytochrome P450, family 2, subfamily b, polypeptide 10 | 1.65 | 4.58 | 5.70 | 8.2e-06 | 1.4e-03 | 3.73 |
| 2268 | 1448451_at | Ak2 | 11637 | adenylate kinase 2 | 0.82 | 9.47 | 5.69 | 8.5e-06 | 1.4e-03 | 3.70 |
| 2744 | 1454799_at | Gpat3 | 231510 | glycerol-3-phosphate acyltransferase 3 | 1.65 | 5.47 | 5.71 | 8.0e-06 | 1.4e-03 | 3.76 |
| 516 | 1420989_at | Cfap97 | 66756 | cilia and flagella associated protein 97 | 1.21 | 5.65 | 5.58 | 1.1e-05 | 1.4e-03 | 3.45 |
| 826 | 1425028_a_at | Tpm2 | 22004 | tropomyosin 2, beta | 1.37 | 6.18 | 5.61 | 1.0e-05 | 1.4e-03 | 3.52 |
| 1171 | 1428988_at | Abcc3 | 76408 | ATP-binding cassette, sub-family C (CFTR/MRP), member 3 | 1.50 | 9.26 | 5.65 | 9.2e-06 | 1.4e-03 | 3.63 |
| 1269 | 1430568_at | Zc3h13 | 67302 | zinc finger CCCH type containing 13 | 1.10 | 4.77 | 5.57 | 1.1e-05 | 1.4e-03 | 3.43 |
| 1545 | 1435312_at | Paqr7 | 71904 | progestin and adipoQ receptor family member VII | 1.39 | 6.01 | 5.56 | 1.1e-05 | 1.4e-03 | 3.42 |
| 1893 | 1438992_x_at | Atf4 | 11911 | activating transcription factor 4 | -0.97 | 8.44 | -5.57 | 1.1e-05 | 1.4e-03 | 3.43 |
| 449 | 1419874_x_at | Zbtb16 | 235320 | zinc finger and BTB domain containing 16 | -2.31 | 6.64 | -5.46 | 1.5e-05 | 1.8e-03 | 3.18 |
| 286 | 1418265_s_at | Irf2 | 16363 | interferon regulatory factor 2 | -0.92 | 8.11 | -5.41 | 1.7e-05 | 1.8e-03 | 3.06 |
| 593 | 1422493_at | Cpox | 12892 | coproporphyrinogen oxidase | 1.07 | 7.83 | 5.39 | 1.8e-05 | 1.8e-03 | 3.01 |
| 730 | 1424133_at | Tmem98 | 103743 | transmembrane protein 98 | 0.88 | 7.01 | 5.41 | 1.7e-05 | 1.8e-03 | 3.06 |
| 856 | 1425392_a_at | Nr1i3 | 12355 | nuclear receptor subfamily 1, group I, member 3 | 0.98 | 7.98 | 5.37 | 1.8e-05 | 1.8e-03 | 2.97 |
| 2602 | 1452378_at | Malat1 | 72289 | metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) | -1.68 | 6.41 | -5.37 | 1.8e-05 | 1.8e-03 | 2.97 |
| 2161 | 1444790_at | Hsbp1l1 | 66255 | heat shock factor binding protein 1-like 1 | -2.09 | 4.71 | -5.34 | 2.0e-05 | 1.9e-03 | 2.89 |
| 151 | 1417126_a_at | Rpl22l1 | 68028 | ribosomal protein L22 like 1 | -0.93 | 10.60 | -5.30 | 2.2e-05 | 2.0e-03 | 2.81 |
| 2486 | 1451322_at | Cmbl | 69574 | carboxymethylenebutenolidase-like (Pseudomonas) | 0.70 | 11.14 | 5.26 | 2.4e-05 | 2.2e-03 | 2.71 |
| 910 | 1426153_a_at | Dsg2 | 13511 | desmoglein 2 | -1.14 | 3.74 | -5.19 | 2.9e-05 | 2.5e-03 | 2.55 |
| 177 | 1417382_at | Entpd5 | 12499 | ectonucleoside triphosphate diphosphohydrolase 5 | 0.89 | 9.87 | 5.17 | 3.0e-05 | 2.6e-03 | 2.50 |
| 280 | 1418230_a_at | Lims1 | 110829 | LIM and senescent cell antigen-like domains 1 | 0.94 | 6.97 | 5.14 | 3.3e-05 | 2.6e-03 | 2.43 |
| 1979 | 1440199_at | Slc25a48 | 328258 | solute carrier family 25, member 48 | 0.85 | 4.76 | 5.15 | 3.2e-05 | 2.6e-03 | 2.44 |
| 2879 | 1456074_at | Sdr9c7 | 70061 | 4short chain dehydrogenase/reductase family 9C, member 7 | -0.89 | 7.22 | -5.13 | 3.3e-05 | 2.6e-03 | 2.42 |
| 453 | 1419915_at | Nus1 | 52014 | NUS1 dehydrodolichyl diphosphate synthase subunit | -0.96 | 4.80 | -5.11 | 3.5e-05 | 2.7e-03 | 2.36 |
| 95 | 1416662_at | Sardh | 192166 | sarcosine dehydrogenase | 0.77 | 10.23 | 5.05 | 4.1e-05 | 3.0e-03 | 2.22 |
| 2970 | 1457721_at | Ppara | 19013 | peroxisome proliferator activated receptor alpha | 0.88 | 9.35 | 5.05 | 4.1e-05 | 3.0e-03 | 2.22 |
| 376 | 1419103_a_at | Abhd6 | 66082 | abhydrolase domain containing 6 | 0.89 | 8.74 | 5.02 | 4.4e-05 | 3.1e-03 | 2.15 |
| 748 | 1424350_s_at | Lpgat1 | 226856 | lysophosphatidylglycerol acyltransferase 1 | 1.17 | 7.74 | 5.02 | 4.4e-05 | 3.1e-03 | 2.15 |
| 2748 | 1454838_s_at | Pkdcc | 106522 | protein kinase domain containing, cytoplasmic | -0.87 | 7.22 | -5.00 | 4.6e-05 | 3.1e-03 | 2.11 |
| 1599 | 1435748_at | Gda | 14544 | guanine deaminase | 0.83 | 8.33 | 4.99 | 4.7e-05 | 3.1e-03 | 2.09 |
| 963 | 1426831_at | Ahcyl1 | 229709 | S-adenosylhomocysteine hydrolase-like 1 | 0.79 | 7.95 | 4.88 | 6.2e-05 | 3.9e-03 | 1.83 |
| 2489 | 1451339_at | Suox | 211389 | sulfite oxidase | 0.80 | 9.69 | 4.89 | 6.1e-05 | 3.9e-03 | 1.84 |
| 588 | 1422438_at | Ephx1 | 13849 | epoxide hydrolase 1, microsomal | 0.88 | 11.05 | 4.85 | 6.7e-05 | 4.2e-03 | 1.75 |
| 409 | 1419456_at | Dcxr | 67880 | dicarbonyl L-xylulose reductase | 0.74 | 10.70 | 4.84 | 6.8e-05 | 4.2e-03 | 1.72 |
| 1807 | 1437868_at | Tent5a | 212943 | terminal nucleotidyltransferase 5A | -1.23 | 7.03 | -4.81 | 7.4e-05 | 4.5e-03 | 1.65 |
| 43 | 1416166_a_at | Prdx4 | 53381 | peroxiredoxin 4 | -1.09 | 9.71 | -4.76 | 8.4e-05 | 4.7e-03 | 1.53 |
| 1866 | 1438562_a_at | Ptpn2 | 19255 | protein tyrosine phosphatase, non-receptor type 2 | -0.78 | 8.10 | -4.75 | 8.6e-05 | 4.7e-03 | 1.51 |
| 2574 | 1452183_a_at | Meg3 | 17263 | maternally expressed 3 | 0.80 | 5.60 | 4.76 | 8.4e-05 | 4.7e-03 | 1.54 |
| 2652 | 1452973_at | Ppm1k | 243382 | protein phosphatase 1K (PP2C domain containing) | 1.10 | 9.67 | 4.78 | 8.0e-05 | 4.7e-03 | 1.57 |
| 2705 | 1453860_s_at | Nr3c1 | 14815 | nuclear receptor subfamily 3, group C, member 1 | 0.78 | 4.59 | 4.76 | 8.5e-05 | 4.7e-03 | 1.52 |
| 2319 | 1449012_s_at | Fndc4 | 64339 | fibronectin type III domain containing 4 | -0.74 | 5.89 | -4.68 | 1.0e-04 | 5.5e-03 | 1.35 |
| 798 | 1424770_at | Cald1 | 109624 | caldesmon 1 | 1.06 | 10.22 | 4.67 | 1.1e-04 | 5.5e-03 | 1.31 |
| 2327 | 1449080_at | Hdac2 | 15182 | histone deacetylase 2 | -1.01 | 6.24 | -4.67 | 1.1e-04 | 5.5e-03 | 1.31 |
| 1108 | 1428547_at | Nt5e | 23959 | 5’ nucleotidase, ecto | 0.91 | 6.10 | 4.65 | 1.1e-04 | 5.7e-03 | 1.27 |
| 2560 | 1452011_a_at | Uxs1 | 67883 | UDP-glucuronate decarboxylase 1 | -0.89 | 7.27 | -4.64 | 1.1e-04 | 5.8e-03 | 1.24 |
| 922 | 1426350_at | Mgat2 | 217664 | mannoside acetylglucosaminyltransferase 2 | -0.95 | 8.37 | -4.60 | 1.2e-04 | 6.0e-03 | 1.16 |
| 1382 | 1433757_a_at | Nisch | 64652 | nischarin | -1.29 | 6.75 | -4.61 | 1.2e-04 | 6.0e-03 | 1.18 |
| 2397 | 1450035_a_at | Prpf40a | 56194 | pre-mRNA processing factor 40A | 1.16 | 6.91 | 4.60 | 1.2e-04 | 6.0e-03 | 1.16 |
| 1857 | 1438473_at | Arl15 | 218639 | ADP-ribosylation factor-like 15 | -0.77 | 5.42 | -4.59 | 1.3e-04 | 6.0e-03 | 1.12 |
| 1975 | 1440134_at | Cyp4a31 | 666168 | cytochrome P450, family 4, subfamily a, polypeptide 31 | 1.43 | 6.74 | 4.59 | 1.3e-04 | 6.0e-03 | 1.13 |
| 397 | 1419382_a_at | Dhrs4 | 28200 | dehydrogenase/reductase (SDR family) member 4 | 0.83 | 9.08 | 4.55 | 1.4e-04 | 6.3e-03 | 1.05 |
| 2110 | 1443695_at | Habp2 | 226243 | hyaluronic acid binding protein 2 | -0.71 | 6.97 | -4.55 | 1.4e-04 | 6.3e-03 | 1.04 |
| 2360 | 1449409_at | Sult1c2 | 69083 | sulfotransferase family, cytosolic, 1C, member 2 | -1.14 | 6.01 | -4.55 | 1.4e-04 | 6.3e-03 | 1.04 |
| 2645 | 1452913_at | Pcp4l1 | 66425 | Purkinje cell protein 4-like 1 | 0.85 | 5.17 | 4.54 | 1.4e-04 | 6.4e-03 | 1.01 |
| 2056 | 1441992_at | Rab14 | 68365 | RAB14, member RAS oncogene family | -1.38 | 5.84 | -4.53 | 1.5e-04 | 6.5e-03 | 0.99 |
| 2291 | 1448649_at | Enpep | 13809 | glutamyl aminopeptidase | -0.87 | 11.03 | -4.50 | 1.6e-04 | 6.9e-03 | 0.91 |
| 569 | 1421957_a_at | Pcyt1a | 13026 | phosphate cytidylyltransferase 1, choline, alpha isoform | 0.72 | 7.22 | 4.46 | 1.8e-04 | 7.3e-03 | 0.83 |
| 2508 | 1451488_at | Fitm1 | 68680 | fat storage-inducing transmembrane protein 1 | 1.26 | 8.55 | 4.46 | 1.8e-04 | 7.3e-03 | 0.83 |
| 562 | 1421852_at | Kcnk5 | 16529 | potassium channel, subfamily K, member 5 | 1.13 | 7.25 | 4.45 | 1.8e-04 | 7.4e-03 | 0.81 |
Tabla 15: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta HF.
Control vs LAR Diet (CTvsLAR):
| X | PROBEID | SYMBOL | ENTREZID | GENENAME | logFC | AveExpr | t | P.Value | adj.P.Val | B |
|---|---|---|---|---|---|---|---|---|---|---|
| 424 | 1419582_at | Cyp2c55 | 72082 | cytochrome P450, family 2, subfamily c, polypeptide 55 | 2.30 | 6.73 | 13.17 | 3.2e-12 | 9.7e-09 | 17.43 |
| 879 | 1425645_s_at | Cyp2b10 | 13088 | cytochrome P450, family 2, subfamily b, polypeptide 10 | 3.23 | 4.58 | 11.16 | 8.7e-11 | 1.3e-07 | 14.49 |
| 848 | 1425314_at | Adgrv1 | 110789 | adhesion G protein-coupled receptor V1 | -2.51 | 6.31 | -10.15 | 5.5e-10 | 5.6e-07 | 12.81 |
| 588 | 1422438_at | Ephx1 | 13849 | epoxide hydrolase 1, microsomal | 1.50 | 11.05 | 8.21 | 2.6e-08 | 1.4e-05 | 9.20 |
| 2355 | 1449375_at | Ces2a | 102022 | carboxylesterase 2A | 1.40 | 11.00 | 8.22 | 2.6e-08 | 1.4e-05 | 9.21 |
| 2815 | 1455454_at | Akr1c19 | 432720 | aldo-keto reductase family 1, member C19 | 1.55 | 9.30 | 8.28 | 2.3e-08 | 1.4e-05 | 9.35 |
| 67 | 1416368_at | Gsta4 | 14860 | glutathione S-transferase, alpha 4 | 1.85 | 9.39 | 8.03 | 3.9e-08 | 1.7e-05 | 8.84 |
| 821 | 1424973_at | Cyp3a25 | 56388 | cytochrome P450, family 3, subfamily a, polypeptide 25 | 1.21 | 12.22 | 7.43 | 1.4e-07 | 5.5e-05 | 7.60 |
| 2544 | 1451814_a_at | Htatip2 | 53415 | HIV-1 Tat interactive protein 2 | 0.94 | 8.80 | 7.03 | 3.6e-07 | 1.2e-04 | 6.72 |
| 520 | 1421040_a_at | Gsta2 | 14858 | glutathione S-transferase, alpha 2 (Yc2) | 2.68 | 10.11 | 6.90 | 4.8e-07 | 1.5e-04 | 6.45 |
| 2431 | 1450715_at | Cyp1a2 | 13077 | cytochrome P450, family 1, subfamily a, polypeptide 2 | 1.34 | 12.30 | 6.80 | 6.1e-07 | 1.7e-04 | 6.22 |
| 846 | 1425303_at | Gck | 103988 | glucokinase | -1.53 | 8.61 | -6.56 | 1.1e-06 | 2.7e-04 | 5.69 |
| 1171 | 1428988_at | Abcc3 | 76408 | ATP-binding cassette, sub-family C (CFTR/MRP), member 3 | 1.71 | 9.26 | 6.42 | 1.5e-06 | 3.5e-04 | 5.37 |
| 215 | 1417761_at | Apoa4 | 11808 | apolipoprotein A-IV | -2.03 | 10.92 | -6.22 | 2.4e-06 | 4.8e-04 | 4.92 |
| 1061 | 1427981_a_at | Csad | 246277 | cysteine sulfinic acid decarboxylase | 2.11 | 9.22 | 6.22 | 2.3e-06 | 4.8e-04 | 4.92 |
| 26 | 1416022_at | Fabp5 | 16592 | fatty acid binding protein 5, epidermal | -3.11 | 8.60 | -6.18 | 2.6e-06 | 5.0e-04 | 4.83 |
| 905 | 1426064_at | Cyp3a44 | 337924 | cytochrome P450, family 3, subfamily a, polypeptide 44 | 1.02 | 3.48 | 6.09 | 3.2e-06 | 5.8e-04 | 4.62 |
| 904 | 1426037_a_at | Rgs16 | 19734 | regulator of G-protein signaling 16 | -4.59 | 7.42 | -5.95 | 4.5e-06 | 7.8e-04 | 4.29 |
| 405 | 1419435_at | Aox1 | 11761 | aldehyde oxidase 1 | 1.11 | 9.61 | 5.80 | 6.5e-06 | 1.1e-03 | 3.94 |
| 62 | 1416308_at | Ugdh | 22235 | UDP-glucose dehydrogenase | 1.16 | 10.19 | 5.75 | 7.2e-06 | 1.1e-03 | 3.84 |
| 177 | 1417382_at | Entpd5 | 12499 | ectonucleoside triphosphate diphosphohydrolase 5 | 0.97 | 9.87 | 5.66 | 9.1e-06 | 1.3e-03 | 3.62 |
| 414 | 1419491_at | Defb1 | 13214 | defensin beta 1 | -1.78 | 6.34 | -5.56 | 1.2e-05 | 1.6e-03 | 3.39 |
| 109 | 1416809_at | Cyp3a11 | 13112 | cytochrome P450, family 3, subfamily a, polypeptide 11 | 1.15 | 13.83 | 5.48 | 1.4e-05 | 1.8e-03 | 3.19 |
| 2587 | 1452277_at | Arsg | 74008 | arylsulfatase G | -1.25 | 6.85 | -5.47 | 1.4e-05 | 1.8e-03 | 3.17 |
| 1034 | 1427474_s_at | Gstm3 | 14864 | glutathione S-transferase, mu 3 | 1.53 | 9.62 | 5.42 | 1.6e-05 | 2.0e-03 | 3.06 |
| 1108 | 1428547_at | Nt5e | 23959 | 5’ nucleotidase, ecto | 1.06 | 6.10 | 5.41 | 1.7e-05 | 2.0e-03 | 3.02 |
| 774 | 1424607_a_at | Gm4354 | 100043316 | predicted gene 4354 | 1.42 | 8.90 | 5.28 | 2.3e-05 | 2.6e-03 | 2.72 |
| 338 | 1418745_at | Omd | 27047 | osteomodulin | -1.31 | 5.78 | -5.20 | 2.8e-05 | 3.1e-03 | 2.54 |
| 2254 | 1448330_at | Gstm1 | 14862 | glutathione S-transferase, mu 1 | 1.02 | 11.76 | 5.16 | 3.1e-05 | 3.3e-03 | 2.45 |
| 305 | 1418438_at | Fabp2 | 14079 | fatty acid binding protein 2, intestinal | -0.96 | 10.57 | -5.02 | 4.4e-05 | 4.4e-03 | 2.09 |
| 374 | 1419094_at | Cyp2c37 | 13096 | cytochrome P450, family 2. subfamily c, polypeptide 37 | 1.03 | 11.64 | 5.03 | 4.3e-05 | 4.4e-03 | 2.12 |
| 2173 | 1445787_at | Ccdc162 | 75973 | coiled-coil domain containing 162 | -0.84 | 5.86 | -4.94 | 5.4e-05 | 5.2e-03 | 1.90 |
| 242 | 1417883_at | Gstt2 | 14872 | glutathione S-transferase, theta 2 | 1.02 | 8.94 | 4.89 | 6.1e-05 | 5.7e-03 | 1.79 |
| 2318 | 1448986_x_at | Dnase2a | 13423 | deoxyribonuclease II alpha | 1.59 | 9.95 | 4.85 | 6.7e-05 | 6.1e-03 | 1.69 |
| 1649 | 1436404_at | Tlcd1 | 68385 | TLC domain containing 1 | -0.84 | 6.66 | -4.77 | 8.2e-05 | 7.2e-03 | 1.50 |
| 2440 | 1450784_at | Reck | 53614 | reversion-inducing-cysteine-rich protein with kazal motifs | -1.22 | 6.30 | -4.74 | 8.8e-05 | 7.5e-03 | 1.44 |
| 355 | 1418857_at | Slc13a2 | 20500 | solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2 | 0.95 | 5.18 | 4.72 | 9.3e-05 | 7.6e-03 | 1.38 |
| 2399 | 1450048_a_at | Idh2 | 269951 | isocitrate dehydrogenase 2 (NADP+), mitochondrial | 0.72 | 8.64 | 4.72 | 9.2e-05 | 7.6e-03 | 1.39 |
| 2142 | 1444242_at | Slco2a1 | 24059 | solute carrier organic anion transporter family, member 2a1 | 0.87 | 5.23 | 4.70 | 9.8e-05 | 7.6e-03 | 1.33 |
| 2219 | 1447791_s_at | Gna14 | 14675 | guanine nucleotide binding protein, alpha 14 | -0.88 | 3.87 | -4.70 | 9.9e-05 | 7.6e-03 | 1.32 |
| 2708 | 1454067_a_at | 4931406C07Rik | 70984 | RIKEN cDNA 4931406C07 gene | 0.86 | 9.72 | 4.64 | 1.1e-04 | 8.5e-03 | 1.19 |
| 376 | 1419103_a_at | Abhd6 | 66082 | abhydrolase domain containing 6 | 0.81 | 8.74 | 4.57 | 1.3e-04 | 9.8e-03 | 1.03 |
| 2161 | 1444790_at | Hsbp1l1 | 66255 | heat shock factor binding protein 1-like 1 | -1.79 | 4.71 | -4.56 | 1.4e-04 | 1.0e-02 | 0.99 |
| 3068 | 1460603_at | Samd9l | 209086 | sterile alpha motif domain containing 9-like | -0.98 | 7.12 | -4.54 | 1.4e-04 | 1.0e-02 | 0.96 |
| 2835 | 1455621_at | Zfp870 | 240066 | zinc finger protein 870 | -0.96 | 3.91 | -4.53 | 1.5e-04 | 1.0e-02 | 0.92 |
| 234 | 1417852_x_at | Clca3a1 | 12722 | chloride channel accessory 3A1 | -1.35 | 5.63 | -4.43 | 1.9e-04 | 1.2e-02 | 0.69 |
| 661 | 1423257_at | Cyp4a14 | 13119 | cytochrome P450, family 4, subfamily a, polypeptide 14 | 3.48 | 8.78 | 4.41 | 2.0e-04 | 1.2e-02 | 0.64 |
| 701 | 1423797_at | Aacs | 78894 | acetoacetyl-CoA synthetase | -1.59 | 7.55 | -4.40 | 2.0e-04 | 1.2e-02 | 0.62 |
| 711 | 1423891_at | Gstt3 | 103140 | glutathione S-transferase, theta 3 | 0.92 | 8.69 | 4.43 | 1.9e-04 | 1.2e-02 | 0.68 |
| 1877 | 1438711_at | Pklr | 18770 | pyruvate kinase liver and red blood cell | -1.70 | 9.23 | -4.42 | 2.0e-04 | 1.2e-02 | 0.66 |
| 1890 | 1438953_at | Vegfd | 14205 | vascular endothelial growth factor D | 0.89 | 5.36 | 4.41 | 2.0e-04 | 1.2e-02 | 0.64 |
| 2248 | 1448300_at | Mgst3 | 66447 | microsomal glutathione S-transferase 3 | 0.83 | 7.99 | 4.41 | 2.0e-04 | 1.2e-02 | 0.65 |
| 2325 | 1449062_at | Khk | 16548 | ketohexokinase | -0.99 | 11.88 | -4.45 | 1.8e-04 | 1.2e-02 | 0.74 |
| 429 | 1419603_at | Ifi204 | 15951 | interferon activated gene 204 | -0.78 | 4.16 | -4.37 | 2.2e-04 | 1.3e-02 | 0.54 |
| 2495 | 1451386_at | Blvrb | 233016 | biliverdin reductase B (flavin reductase (NADPH)) | 0.68 | 10.34 | 4.36 | 2.2e-04 | 1.3e-02 | 0.53 |
| 569 | 1421957_a_at | Pcyt1a | 13026 | phosphate cytidylyltransferase 1, choline, alpha isoform | 0.70 | 7.22 | 4.33 | 2.4e-04 | 1.3e-02 | 0.46 |
| 10 | 1415840_at | Elovl5 | 68801 | ELOVL family member 5, elongation of long chain fatty acids (yeast) | -0.84 | 12.87 | -4.30 | 2.6e-04 | 1.4e-02 | 0.38 |
| 664 | 1423266_at | Prxl2b | 66469 | peroxiredoxin like 2B | 0.76 | 8.16 | 4.31 | 2.6e-04 | 1.4e-02 | 0.41 |
| 1008 | 1427202_at | Etfbkmt | 320204 | electron transfer flavoprotein beta subunit lysine methyltransferase | 1.17 | 8.29 | 4.30 | 2.6e-04 | 1.4e-02 | 0.38 |
| 1643 | 1436293_x_at | Ildr2 | 100039795 | immunoglobulin-like domain containing receptor 2 | 1.16 | 7.86 | 4.30 | 2.7e-04 | 1.4e-02 | 0.37 |
| 1172 | 1429001_at | Pir | 69656 | pirin | 0.76 | 7.40 | 4.29 | 2.7e-04 | 1.4e-02 | 0.35 |
| 1023 | 1427356_at | Fam89a | 69627 | family with sequence similarity 89, member A | 1.10 | 6.32 | 4.28 | 2.8e-04 | 1.4e-02 | 0.32 |
| 2887 | 1456156_at | Lepr | 16847 | leptin receptor | -2.34 | 5.12 | -4.24 | 3.0e-04 | 1.5e-02 | 0.24 |
| 2546 | 1451860_a_at | Trim30a | 20128 | tripartite motif-containing 30A | -0.88 | 5.66 | -4.23 | 3.2e-04 | 1.5e-02 | 0.20 |
| 525 | 1421092_at | Serpina12 | 68054 | serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12 | -1.64 | 10.58 | -4.18 | 3.6e-04 | 1.7e-02 | 0.08 |
| 921 | 1426278_at | Ifi27l2a | 76933 | interferon, alpha-inducible protein 27 like 2A | -1.12 | 6.87 | -4.17 | 3.6e-04 | 1.7e-02 | 0.07 |
| 1456 | 1434437_x_at | Rrm2 | 20135 | ribonucleotide reductase M2 | -1.63 | 6.22 | -4.17 | 3.7e-04 | 1.7e-02 | 0.07 |
| 2955 | 1457403_at | 9130409I23Rik | 619326 | RIKEN cDNA 9130409I23 gene | 1.75 | 7.06 | 4.18 | 3.6e-04 | 1.7e-02 | 0.10 |
| 313 | 1418492_at | Grem2 | 23893 | gremlin 2, DAN family BMP antagonist | -1.20 | 5.92 | -4.13 | 4.1e-04 | 1.8e-02 | -0.03 |
| 2471 | 1451139_at | Slc39a4 | 72027 | solute carrier family 39 (zinc transporter), member 4 | 1.04 | 7.90 | 4.13 | 4.0e-04 | 1.8e-02 | -0.02 |
| 2005 | 1440739_at | Vegfc | 22341 | vascular endothelial growth factor C | -0.72 | 5.75 | -4.12 | 4.1e-04 | 1.8e-02 | -0.05 |
| 1840 | 1438242_at | Usp40 | 227334 | ubiquitin specific peptidase 40 | 0.72 | 5.88 | 4.10 | 4.3e-04 | 1.9e-02 | -0.10 |
| 2288 | 1448620_at | Fcgr3 | 14131 | Fc receptor, IgG, low affinity III | -0.91 | 6.37 | -4.07 | 4.7e-04 | 2.0e-02 | -0.17 |
| 2874 | 1456036_x_at | Gsto1 | 14873 | glutathione S-transferase omega 1 | 0.76 | 10.50 | 4.07 | 4.7e-04 | 2.0e-02 | -0.17 |
| 2574 | 1452183_a_at | Meg3 | 17263 | maternally expressed 3 | 0.69 | 5.60 | 4.06 | 4.8e-04 | 2.0e-02 | -0.19 |
Tabla 16: toptable que contiene los 75 genes con una mayor evidencia de estar diferencialmente expresados entre la dieta control y la dieta LAR.
Las tablas de genes diferencialmente expresados (conocidas también como toptables) tienen la misma debilidad y el mismo punto fuerte: contienen demasiada información. Una alternativa más visual para identificar cuan diferencialmente expresados están los genes de cada comparación es mediante el uso de volcano plots. A continuación se muestran los volcano plots para cada una de las 8 comparaciones (Figura 4). Para facilitar su interpretación se han añadido una línea horizontal con el fdr cutoff (FDR = 0.1), dos líneas verticales con los foldChange cutoffs (FC = -2, 2) y una leyenda de colores (NS = gris, log2FC = verde, p-value = azul, p-value & log2FC = rojo).
Tanto los datos de las toptables como los de los volcano plots parecen indicar que las dietas que presentan una mayor variación en la expresión respecto el control son AR, DR y AC mientras las dietas con menor variación parecen ser DHA, FR y LAR. Estos resultados secundan el patrón que observamos en el PCA plot de los datos normalizados (Figura 2).
Figura 4: volcano plots resultantes de las comparaciones de la dieta control con cada una de las otras 8 dietas por separado. Se consideran diferencialmente expresados los genes que corresponden a los puntos de color rojo.
Podemos complementar los resultados de las toptables y los volcano plots construyendo una tabla resumen que contenga, para cada comparación, el número de genes sobrexpresados (log2FC > 1 & p-valor ajustado < 0.1), infraexpresados (log2FC < 1 & p-valor ajustado < 0.1) o aquellos que no varían su expresión (log2FC \(\in [-1, 1]\) | p-valor ajustado > 0.1). La Tabla 17 muestra el contenido de esta tabla resumen. Observamos que, tal y como se ha propuesto anteriormente, las dietas que presentan mayor cantidad de genes diferencialmente expresados respecto al control son DR (573), AR (283) y AC (178). Las dietas que presentan menor cantidad de genes son DHA (7), **FR (33) y EFA (72).
| X | CTvsFR | CTvsAC | CTvsAR | CTvsDHA | CTvsDR | CTvsEFA | CTvsHF | CTvsLAR |
|---|---|---|---|---|---|---|---|---|
| Down | 25 | 107 | 100 | 6 | 317 | 14 | 52 | 48 |
| NotSig | 886 | 741 | 636 | 912 | 346 | 847 | 818 | 833 |
| Up | 8 | 71 | 183 | 1 | 256 | 58 | 49 | 38 |
Tabla 17: genes sobreexpresados (Up), infraexpresados (Down) y aquellos que no presentan variación en su expresión (NotSig) para cada una de las 8 dietas (respecto al control).
Tras seleccionar los genes diferencialmente expresados en almenos una de las comparaciones (1333), podemos construir un heatmap para comparar los patrones de expresión entre muestras/dietas y agruparlas en clústers en función de su similaridad (Figura 5). Si observamos detalladamente los resultados, identificamos, en primer lugar, que hay dos dietas cuyos patrones difieren claramente del resto y entre ellas. Nos referimos a DR y AR. En relación al resto de dietas, observamos que todas ellas están contenidas en un único macroclúster. Un análisis más detallado muestra que este macroclúster está formado por dos subclústers, uno que contiene las dietas AC, LAR y HF (subclúster 1) y otro que contiene las dietas DHA, CT, FR y EFA (subclúster 2). Si queremos profundizar aún más, podríamos afirmar que el subclúster 1 está constituido por dos subclústers adicionales, uno que contiene AC (subclúster 1.1) y otro que contiene LAR y HF (subclúster 1.2). En referencia al subclúster 2, este también puede ser segregado en dos subclústers más pequeños, uno que contiene los grupos CT y DHA (subclúster 2.1) y uno que contiene los grupos FR y EFA (subclúster 2.2). En cualquier caso, la información más valiosa que podemos extraer de este gráfico es que las dietas más parecidas al control son de más a menos: DHA, EFA y FR y las dietas más alejadas del control son de más a menos: DR, AR y AC.
Figura 5: comparación, mediante un heatmap, de los patrones de expresión de los genes diferencialmente expresados almenos entre 2 de las 9 dietas.
Ahora que ya hemos agrupado las dietas, podemos estudiar cuantos genes diferencialmente expresados respecto al control comparten las dietas de un mismo clúster. A continuación se muestran 2 diagramas de Venn, uno para el subclúster 1 y uno para el subclúster 2. En primer lugar, vamos a analizar los resultados correspondientes al clúster 1 (Figura 6A). Observamos que, respecto al control, las dietas AC y LAR comparten 23 genes diferencialmente expresados. Adicionalmente, las dietas LAR y HF comparten 20 genes, las dietas AC y HF 39 y las tres dietas 11. En cuanto al clúster 2, las dietas FR y DHA comparten 1 gene, las dietas EFA y DHA también 1 gen, las dietas FR y EFA comparten 7 genes y, finalmente, las tres dietas comparten 1 gen.
Figura 6: diagrama de Venn que muestra los genes en común entre las comparaciones de cada una de las dietas del clúster 1 y el control (A). Diagrama de Venn que muestra los genes en común entre las comparaciones de cada una de las dietas del clúster 2 y el control.
Una enfoque más apropiado para analizar estos resultados consiste en determinar que porcentaje o proporción de genes de una comparación se encuentra en otra. Mediante simples cálculos obtenemos los siguientes resultados:
Clúster 1:
Clúster 2:
Aunque ya conocemos que genes están sobrexpresados o infraexpresados respecto al control en cada una de las dietas, es difícil extraer conclusiones a partir de esta información. Con el objetivo de obtener una visión más general e identificar que vías metabólicas se ven modificadas por cada dieta se ha realizado un análisis de significación o de pathways. Este tipo de análisis permiten clasificar y agrupar los genes diferencialmente expresados dentro de las vías metabólicas en las que participan. A continuación se muestra, para cada dieta, una tabla que contiene los resultados de este análisis (Tablas 18-24). Es importante destacar que la comparación CTvsDHA no se ha incluido porque el número insuficiente de genes diferencialmente expresados no ha permitido realizar el análisis.
Control vs 60% Fructose (CTvsFR):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-75105 | Fatty acyl-CoA biosynthesis | 6/154 | 33/8772 | 2e-05 | 1.1e-02 | 1.1e-02 | 6 |
Tabla 18: vías metabólicas expresadas diferencialmente entre el control y la dieta HF.
Control vs Adjusted Calories Diet (CTvsAC):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-191273 | Cholesterol biosynthesis | 16/484 | 25/8772 | 7.5e-15 | 6.3e-12 | 6.0e-12 | 16 |
| R-MMU-8978868 | Fatty acid metabolism | 32/484 | 169/8772 | 5.5e-10 | 1.7e-07 | 1.6e-07 | 32 |
| R-MMU-8957322 | Metabolism of steroids | 27/484 | 125/8772 | 6.1e-10 | 1.7e-07 | 1.6e-07 | 27 |
| R-MMU-2046104 | alpha-linolenic (omega3) and linoleic (omega6) acid metabolism | 7/484 | 14/8772 | 3.6e-06 | 6.1e-04 | 5.8e-04 | 7 |
| R-MMU-2046106 | alpha-linolenic acid (ALA) metabolism | 7/484 | 14/8772 | 3.6e-06 | 6.1e-04 | 5.8e-04 | 7 |
| R-MMU-9033241 | Peroxisomal protein import | 14/484 | 64/8772 | 7.5e-06 | 1.0e-03 | 1.0e-03 | 14 |
| R-MMU-9609507 | Protein localization | 18/484 | 105/8772 | 1.5e-05 | 1.8e-03 | 1.7e-03 | 18 |
| R-MMU-211945 | Phase I - Functionalization of compounds | 18/484 | 108/8772 | 2.2e-05 | 2.3e-03 | 2.2e-03 | 18 |
| R-MMU-174824 | Plasma lipoprotein assembly, remodeling, and clearance | 12/484 | 57/8772 | 5.0e-05 | 4.7e-03 | 4.5e-03 | 12 |
| R-MMU-390918 | Peroxisomal lipid metabolism | 8/484 | 28/8772 | 9.4e-05 | 7.9e-03 | 7.6e-03 | 8 |
| R-MMU-8964038 | LDL clearance | 6/484 | 16/8772 | 1.4e-04 | 1.0e-02 | 9.9e-03 | 6 |
| R-MMU-196854 | Metabolism of vitamins and cofactors | 23/484 | 182/8772 | 1.6e-04 | 1.1e-02 | 1.0e-02 | 23 |
| R-MMU-8979227 | Triglyceride metabolism | 7/484 | 23/8772 | 1.7e-04 | 1.1e-02 | 1.0e-02 | 7 |
| R-MMU-1483191 | Synthesis of PC | 7/484 | 24/8772 | 2.3e-04 | 1.4e-02 | 1.3e-02 | 7 |
| R-MMU-75105 | Fatty acyl-CoA biosynthesis | 8/484 | 33/8772 | 3.3e-04 | 1.8e-02 | 1.8e-02 | 8 |
| R-MMU-166663 | Initial triggering of complement | 6/484 | 20/8772 | 5.5e-04 | 2.9e-02 | 2.7e-02 | 6 |
| R-MMU-8964043 | Plasma lipoprotein clearance | 7/484 | 28/8772 | 6.4e-04 | 3.2e-02 | 3.0e-02 | 7 |
| R-MMU-977068 | Termination of O-glycan biosynthesis | 5/484 | 15/8772 | 9.5e-04 | 4.2e-02 | 4.0e-02 | 5 |
| R-MMU-75876 | Synthesis of very long-chain fatty acyl-CoAs | 6/484 | 22/8772 | 9.6e-04 | 4.2e-02 | 4.0e-02 | 6 |
Tabla 19: vías metabólicas expresadas diferencialmente entre el control y la dieta AC.
Control vs Atherogenic Rodent Diet (CTvsAR):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-191273 | Cholesterol biosynthesis | 17/591 | 25/8772 | 6.3e-15 | 5.5e-12 | 5.3e-12 | 17 |
| R-MMU-8957322 | Metabolism of steroids | 34/591 | 125/8772 | 8.3e-13 | 3.6e-10 | 3.4e-10 | 34 |
| R-MMU-211859 | Biological oxidations | 39/591 | 202/8772 | 1.4e-09 | 3.3e-07 | 3.2e-07 | 39 |
| R-MMU-211945 | Phase I - Functionalization of compounds | 27/591 | 108/8772 | 1.5e-09 | 3.3e-07 | 3.2e-07 | 27 |
| R-MMU-8978868 | Fatty acid metabolism | 31/591 | 169/8772 | 2.4e-07 | 4.2e-05 | 4.0e-05 | 31 |
| R-MMU-2046104 | alpha-linolenic (omega3) and linoleic (omega6) acid metabolism | 7/591 | 14/8772 | 1.4e-05 | 1.6e-03 | 1.5e-03 | 7 |
| R-MMU-2046106 | alpha-linolenic acid (ALA) metabolism | 7/591 | 14/8772 | 1.4e-05 | 1.6e-03 | 1.5e-03 | 7 |
| R-MMU-211897 | Cytochrome P450 - arranged by substrate type | 16/591 | 71/8772 | 1.4e-05 | 1.6e-03 | 1.5e-03 | 16 |
| R-MMU-75105 | Fatty acyl-CoA biosynthesis | 10/591 | 33/8772 | 4.0e-05 | 3.9e-03 | 3.7e-03 | 10 |
| R-MMU-75876 | Synthesis of very long-chain fatty acyl-CoAs | 8/591 | 22/8772 | 5.6e-05 | 4.8e-03 | 4.6e-03 | 8 |
| R-MMU-196854 | Metabolism of vitamins and cofactors | 27/591 | 182/8772 | 8.1e-05 | 6.3e-03 | 6.1e-03 | 27 |
| R-MMU-194068 | Bile acid and bile salt metabolism | 11/591 | 44/8772 | 1.2e-04 | 8.5e-03 | 8.1e-03 | 11 |
| R-MMU-8979227 | Triglyceride metabolism | 7/591 | 23/8772 | 5.8e-04 | 3.8e-02 | 3.7e-02 | 7 |
| R-MMU-156590 | Glutathione conjugation | 8/591 | 31/8772 | 8.0e-04 | 4.9e-02 | 4.7e-02 | 8 |
Tabla 20: vías metabólicas expresadas diferencialmente entre el control y la dieta AR.
Control vs Diet-Restriction (CTvsDR):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-8978868 | Fatty acid metabolism | 48/885 | 169/8772 | 1.3e-11 | 1.2e-08 | 1.2e-08 | 48 |
| R-MMU-191273 | Cholesterol biosynthesis | 14/885 | 25/8772 | 1.6e-08 | 7.5e-06 | 7.4e-06 | 14 |
| R-MMU-211859 | Biological oxidations | 46/885 | 202/8772 | 7.6e-08 | 2.4e-05 | 2.4e-05 | 46 |
| R-MMU-211945 | Phase I - Functionalization of compounds | 29/885 | 108/8772 | 5.6e-07 | 1.3e-04 | 1.3e-04 | 29 |
| R-MMU-200425 | Import of palmitoyl-CoA into the mitochondrial matrix | 9/885 | 14/8772 | 1.3e-06 | 2.5e-04 | 2.4e-04 | 9 |
| R-MMU-8957322 | Metabolism of steroids | 30/885 | 125/8772 | 4.6e-06 | 7.3e-04 | 7.1e-04 | 30 |
| R-MMU-166663 | Initial triggering of complement | 10/885 | 20/8772 | 7.5e-06 | 1.0e-03 | 1.0e-03 | 10 |
| R-MMU-211897 | Cytochrome P450 - arranged by substrate type | 20/885 | 71/8772 | 1.5e-05 | 1.7e-03 | 1.7e-03 | 20 |
| R-MMU-166658 | Complement cascade | 15/885 | 48/8772 | 4.5e-05 | 4.8e-03 | 4.7e-03 | 15 |
| R-MMU-211958 | Miscellaneous substrates | 10/885 | 26/8772 | 1.2e-04 | 1.2e-02 | 1.1e-02 | 10 |
| R-MMU-1483206 | Glycerophospholipid biosynthesis | 25/885 | 115/8772 | 1.6e-04 | 1.3e-02 | 1.3e-02 | 25 |
| R-MMU-166786 | Creation of C4 and C2 activators | 7/885 | 14/8772 | 1.9e-04 | 1.3e-02 | 1.3e-02 | 7 |
| R-MMU-2046104 | alpha-linolenic (omega3) and linoleic (omega6) acid metabolism | 7/885 | 14/8772 | 1.9e-04 | 1.3e-02 | 1.3e-02 | 7 |
| R-MMU-2046106 | alpha-linolenic acid (ALA) metabolism | 7/885 | 14/8772 | 1.9e-04 | 1.3e-02 | 1.3e-02 | 7 |
| R-MMU-196854 | Metabolism of vitamins and cofactors | 34/885 | 182/8772 | 2.7e-04 | 1.7e-02 | 1.7e-02 | 34 |
| R-MMU-1483213 | Synthesis of PE | 6/885 | 12/8772 | 5.6e-04 | 3.3e-02 | 3.3e-02 | 6 |
Tabla 21: vías metabólicas expresadas diferencialmente entre el control y la dieta DR.
Control vs EFA-Deficient Diet (CTvsEFA):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-191273 | Cholesterol biosynthesis | 8/224 | 25/8772 | 1.2e-07 | 7.9e-05 | 7.7e-05 | 8 |
| R-MMU-8957322 | Metabolism of steroids | 14/224 | 125/8772 | 3.3e-06 | 1.1e-03 | 1.1e-03 | 14 |
| R-MMU-8979227 | Triglyceride metabolism | 6/224 | 23/8772 | 1.8e-05 | 4.1e-03 | 3.9e-03 | 6 |
| R-MMU-163560 | Triglyceride catabolism | 4/224 | 11/8772 | 1.2e-04 | 2.0e-02 | 1.9e-02 | 4 |
| R-MMU-75105 | Fatty acyl-CoA biosynthesis | 6/224 | 33/8772 | 1.6e-04 | 2.2e-02 | 2.1e-02 | 6 |
Tabla 22: vías metabólicas expresadas diferencialmente entre el control y la dieta EFA.
Control vs High fat Diet (CTvsHF):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-8978868 | Fatty acid metabolism | 26/423 | 169/8772 | 1.2e-07 | 1.0e-04 | 1.0e-04 | 26 |
| R-MMU-9613829 | Chaperone Mediated Autophagy | 7/423 | 22/8772 | 5.2e-05 | 2.2e-02 | 2.1e-02 | 7 |
| R-MMU-191273 | Cholesterol biosynthesis | 7/423 | 25/8772 | 1.3e-04 | 3.6e-02 | 3.5e-02 | 7 |
Tabla 23: vías metabólicas expresadas diferencialmente entre el control y la dieta HF.
Control vs LAR Diet (CTvsLAR):
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | Count |
|---|---|---|---|---|---|---|---|
| R-MMU-211859 | Biological oxidations | 21/270 | 202/8772 | 9.6e-07 | 5.3e-04 | 5.1e-04 | 21 |
| R-MMU-8978868 | Fatty acid metabolism | 18/270 | 169/8772 | 4.1e-06 | 1.1e-03 | 1.1e-03 | 18 |
| R-MMU-211945 | Phase I - Functionalization of compounds | 13/270 | 108/8772 | 2.5e-05 | 4.6e-03 | 4.5e-03 | 13 |
| R-MMU-200425 | Import of palmitoyl-CoA into the mitochondrial matrix | 5/270 | 14/8772 | 4.2e-05 | 5.8e-03 | 5.6e-03 | 5 |
| R-MMU-8979227 | Triglyceride metabolism | 6/270 | 23/8772 | 5.2e-05 | 5.8e-03 | 5.6e-03 | 6 |
| R-MMU-163560 | Triglyceride catabolism | 4/270 | 11/8772 | 2.4e-04 | 2.3e-02 | 2.2e-02 | 4 |
| R-MMU-75105 | Fatty acyl-CoA biosynthesis | 6/270 | 33/8772 | 4.4e-04 | 3.3e-02 | 3.2e-02 | 6 |
| R-MMU-196854 | Metabolism of vitamins and cofactors | 15/270 | 182/8772 | 4.8e-04 | 3.3e-02 | 3.2e-02 | 15 |
| R-MMU-2046104 | alpha-linolenic (omega3) and linoleic (omega6) acid metabolism | 4/270 | 14/8772 | 6.9e-04 | 3.8e-02 | 3.7e-02 | 4 |
| R-MMU-2046106 | alpha-linolenic acid (ALA) metabolism | 4/270 | 14/8772 | 6.9e-04 | 3.8e-02 | 3.7e-02 | 4 |
| R-MMU-196849 | Metabolism of water-soluble vitamins and cofactors | 11/270 | 118/8772 | 9.9e-04 | 5.0e-02 | 4.8e-02 | 11 |
Tabla 24: vías metabólicas expresadas diferencialmente entre el control y la dieta LAR.
De forma análoga a las toptables, las pathway tables también contienen demasiada información. Una solución mucho más visual consiste en construir un cnetplot para cada comparación. A continuación se muestran los cnetplots corresondientes a cada una de las tablas que se acaban de presentar (Figura 7).
Figura 7: cnetplots que muestran las vías metabólicas con mayor evidencia de estar diferencialmente expresadas entre el control y las dietas FR (A), AC (B), AR (C), DR (D), EFA (E), HF (F) y LAR (G).
Empezaremos por comentar los resultados de cada dieta por separado. En la lista presentada a continuación se indican cuáles son las vías con mayor evidencia de estar diferencialmente expresadas respecto al control, especificando si estas están sobrexpresadas, infraexpresadas o si presentan, en proporciones similares, genes en ambas direcciones.
Por otro lado, puede resultar interesante comparar que vías comparten o no las dietas de los anteriormente definidos clúster 1 y clúster 2. En relación al clúster 1 (AC, HF, LAR), de las cuatro vías que presentan una mayor evidencia de estar diferencialmente expresadas, solo comparten el metabolismo de ácidos grasos. A esta vía se le añade la síntesis de colesterol si solo consideramos las dietas AC y HF. Resulta destacable que, aún cuando el metabolismo de ácidos grasos presenta genes expresados en ambas direcciones para las condiciones AC y HF, esté significativamente infraexpresado para la dieta LAR. También cabe remarcar que mientras para la dieta HF los genes involucrados en la síntesis de colesterol no presentan una sobrexpresión demasiado accentuada, si la presentan para la dieta AC. En cuanto al clúster 2 (FR y EFA), las dos dietas comparten la única vía diferencialmente expresada en FR, estando, además, sobrexpresada en ambas condiciones.
En cualquier proyecto de investigación, la discusión de los resultados y la extracción de conclusiones requieren de un conocimiento exhaustivo del contexto biológico del estudio. Sin embargo, obtener el grado adecuado de este conocimiento puede implicar meses o años realizando investigación en una misma dirección. Por ese motivo, con mucha frecuencia, el papel del bioinformático pasa a un segundo plano en esta parte del estudio. Su papel, pues, consiste básicamente en generar un informe con los resultados y, dentro de lo posible, comentarlos. Considerando que en la sección de resultados ya hemos realizado una breve discusión de estos y que, debido a la gran cantidad de grupos la complejidad del estudio que hemos escogido es considerable, hemos decidido enfocar la discusión desde un punto de vista más valorativo.
A lo largo de la redacción de este informe nos hemos basado principalmente en los métodos propuestos por el personal docente que coordina esta asignatura. Si bien es verdad que en algunas situaciones se han buscado alternativas más completas, en la mayoría de casos se ha intentado seguir las pautas establecidas. Sin embargo, la velocidad con la que avanzan las diferentes ramas de la bioinformática y la aparición constante de nuevos paquetes hace que algunas de las librerías utilizadas en el estudio no sean las más óptimas. Por ejemplo, la función EnhancedVolcano() del paquete con el mismo nombre resulta una alternativa mucho más completa y visual que la función volcanoplot() del paquete limma. Por otro lado, en relación al análisis de pathways, aunque el profesorado planteó una alternativa possible al paquete ReactomePA (clusterProfiler), por un tema de simplicidad y tiempo nos decidimos a utilizar el que había sido propuesto en primer lugar.
Es obvio que si hubiéramos dispuesto de más tiempo o tubiéramos un conocimiento más detallado de la temática del estudio la discusión de los resultados y la elaboración de conclusiones hubiera sido mucho más profunda. Sin embargo, esta PEC ha sido un ejercicio muy enriquecedor, y nos ha ayudado a establecer un primer contacto con los análisis de datos de microarrays a la vez que perfeccionábamos la construcción de informes dinámicos con RMarkdown.
plotPCA3 <- function (datos, labels, factor, title, scale, size = 1.5, glineas = 0.25) {
data <- prcomp(t(datos), scale = scale)
# plot adjustments
dataDf <- data.frame(data$x)
Group <- factor
loads <- round(data$sdev^2/sum(data$sdev^2) * 100, 1)
# main plot
p1 <- ggplot(data = dataDf, aes(x = PC1, y = PC2)) +
theme_classic() +
geom_hline(yintercept = 0, color = "gray70") +
geom_vline(xintercept = 0, color = "gray70") +
geom_point(aes(color = Group), size = 2) +
coord_cartesian(xlim = c(min(data$x[ , 1]) - 5, max(data$x[ , 1]) + 5)) +
scale_fill_discrete(name = "Group") +
theme(axis.title.y = element_text(size = 10,
margin = margin(t = 0, r = 10, b = 0, l = 0)),
axis.title.x = element_text(size = 10,
margin = margin(t = 10, r = 0, b = 0, l = 0)),
axis.text = element_text(size = 7),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10),
legend.key.size = unit(0.4, "cm"),
legend.key.width = unit(0.5,"cm"))
# avoiding labels superposition
p1 + geom_text_repel(aes(y = PC2 + 0.25, label = labels), segment.size = 0.25, size = size) +
labs(x = c(paste("PC1", loads[1], "%")), y = c(paste("PC2", loads[2], "%"))) +
ggtitle(paste("Principal Component Analysis for: ", title, sep = " ")) +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis(discrete = T)
}
Figura S1: Código correspondiente a la función plotPCA3().
annotatedTopTable <- function(topTab, anotPackage){
topTab <- cbind(PROBEID = rownames(topTab), topTab)
myProbes <- rownames(topTab)
thePackage <- eval(parse(text = anotPackage))
geneAnots <- select(thePackage,
myProbes,
c("SYMBOL", "ENTREZID", "GENENAME"))
annotatedTopTab <- merge(x = geneAnots,
y = topTab, by.x = "PROBEID",
by.y = "PROBEID")
return(annotatedTopTab)
}
Figura S2: Código correspondiente a la función annotatedTopTable().
Blighe, Rana &. 2019. EnhancedVolcano: Publication-Ready Volcano Plots with Enhanced Colouring and Labeling. https://github.com/kevinblighe/EnhancedVolcano.
Carlson, Marc. 2016. Mouse4302.db: Affymetrix Mouse Genome 430 2.0 Array Annotation Data (Chip Mouse4302).
Carvalho, Irizarry &. 2010. “A Framework for Oligonucleotide Microarray Preprocessing.” Bioinformatics 26 (19): 2363–7. https://doi.org/10.1093/bioinformatics/btq431.
Chrominski, Tkacz &. 2015. “Comparison of High-Level Microarray Analysis Methods in the Context of Result Consistency.” Edited by Ken Mills. PLOS ONE 10 (6): e0128845. https://doi.org/10.1371/journal.pone.0128845.
Depiereux, De Meulder &. 2015. “Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout.” Edited by Gen Hua Yue. PLOS ONE 10 (7): e0128598. https://doi.org/10.1371/journal.pone.0128598.
Draghici, Kuklin &. 2001. “Experimental Design, Analysis of Variance and Slide Quality Assessment in Gene Expression Arrays.” Current Opinion in Drug Discovery & Development 4 (June): 332–7.
Gan, Stowe &. 2014. “Using Kepler for Tool Integration in Microarray Analysis Workflows.” Procedia Computer Science 29: 2162–7. https://doi.org/10.1016/j.procs.2014.05.201.
Gentleman, Carey &. 2019. Genefilter: Genefilter: Methods for Filtering Genes from High-Throughput Experiments.
Irizarry, R. A. 2003. “Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data.” Biostatistics 4 (2): 249–64. https://doi.org/10.1093/biostatistics/4.2.249.
Kauffmann, Huber &. 2009. “ArrayQualityMetrics–a Bioconductor Package for Quality Assessment of Microarray Data.” Bioinformatics 25 (3): 415–6.
Klaus, Reisenauer &. 2018. “An End to End Workflow for Differential Gene Expression Using Affymetrix Microarrays.” F1000Research 5 (July): 1384. https://doi.org/10.12688/f1000research.8967.2.
Levant, Ozias &. 2006. “Diet (n-3) Polyunsaturated Fatty Acid Content and Parity Interact to Alter Maternal Rat Brain Phospholipid Fatty Acid Composition.” The Journal of Nutrition 136 (8): 2236–42. https://doi.org/10.1093/jn/136.8.2236.
Mehta, Rani &. 2011. “Software and Tools for Microarray Data Analysis.” In Gene Expression Profiling: Methods and Protocols, edited by Lorraine O’Driscoll, 41–53. Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-61779-289-2_4.
RCoreTeam. 2019. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Renaud, Julia Y. AND Lu, Helen J. AND Cui. 2014. “Effect of Diet on Expression of Genes Involved in Lipid Metabolism, Oxidative Stress, and Inflammation in Mouse Liver–Insights into Mechanisms of Hepatic Steatosis.” PLOS ONE 9 (2): 1–17. https://doi.org/10.1371/journal.pone.0088584.
Smyth, Gordon K. 2004. “Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments.” Statistical Applications in Genetics and Molecular Biology 3 (1): 1–25. https://doi.org/10.2202/1544-6115.1027.
Smyth, Ritchie &. 2015. “limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies.” Nucleic Acids Research 43 (7): e47. https://doi.org/10.1093/nar/gkv007.
Tsai, C.-A. 2003. “Testing for Differentially Expressed Genes with Microarray Data.” Nucleic Acids Research 31 (9): 52e–52. https://doi.org/10.1093/nar/gng052.
Varady, Roohk &. 2007. “Effects of Modified Alternate-Day Fasting Regimens on Adipocyte Size, Triglyceride Metabolism, and Plasma Adiponectin Levels in Mice.” Journal of Lipid Research 48 (10): 2212–9. https://doi.org/10.1194/jlr.m700223-jlr200.
Warnes, Bolker &. 2020. Gplots: Various R Programming Tools for Plotting Data. https://CRAN.R-project.org/package=gplots.
Yu, Guangchuang. 2019. Enrichplot: Visualization of Functional Enrichment Result. https://github.com/GuangchuangYu/enrichplot.
Yu, Qing-Yu &. 2016. “ReactomePA: An R/Bioconductor Package for Reactome Pathway Analysis and Visualization.” Molecular BioSystems 12 (12): 477–79. https://doi.org/10.1039/C5MB00663E.
Yu, Wang &. 2015. “DOSE: An R/Bioconductor Package for Disease Ontology Semantic and Enrichment Analysis.” Bioinformatics 31 (4): 608–9. https://doi.org/10.1093/bioinformatics/btu684.